rm(list=ls())
# Set the working directory to where folders named after the samples are located.
# The folder contains spliced.mtx, unspliced.mtx, barcodes and gene id files, and json files produced by scKB that documents the sequencing stats.
setwd("/scratch/AG_Ohler/CheWei/scKB")
library(tidyverse)
library(Seurat)
library(RColorBrewer)
library(future)
library(cowplot)
library(ComplexHeatmap)
library(circlize)
library(ggrepel)
#for 200gb ram
options(future.globals.maxSize = 200000 * 1024^2)
── Attaching packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.0 ── ✔ ggplot2 3.3.2 ✔ purrr 0.3.4 ✔ tibble 3.0.4 ✔ dplyr 1.0.2 ✔ tidyr 1.1.2 ✔ stringr 1.4.0 ✔ readr 1.4.0 ✔ forcats 0.5.0 ── Conflicts ───────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() Loading required package: grid ======================================== ComplexHeatmap version 2.6.2 Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/ Github page: https://github.com/jokergoo/ComplexHeatmap Documentation: http://jokergoo.github.io/ComplexHeatmap-reference If you use it in published research, please cite: Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 2016. This message can be suppressed by: suppressPackageStartupMessages(library(ComplexHeatmap)) ======================================== ======================================== circlize version 0.4.12 CRAN page: https://cran.r-project.org/package=circlize Github page: https://github.com/jokergoo/circlize Documentation: https://jokergoo.github.io/circlize_book/book/ If you use it in published research, please cite: Gu, Z. circlize implements and enhances circular visualization in R. Bioinformatics 2014. This message can be suppressed by: suppressPackageStartupMessages(library(circlize)) ========================================
rc.integrated <- readRDS("./supp_data/Ground_Tissue_Atlas.rds")
table(rc.integrated$celltype.anno)
Quiescent Center Columella
158 0
Lateral Root Cap Atrichoblast
0 0
Trichoblast Cortex
0 11073
Endodermis Metaphloem & Companion Cell
11369 0
Protophloem Procambium
0 0
Xylem Pole Pericycle Phloem Pole Pericycle
0 0
Protoxylem Metaxylem
0 0
# Plot celltype annotation
order <- c("Quiescent Center", "Ground Tissue","Columella", "Lateral Root Cap", "Atrichoblast", "Trichoblast", "Cortex", "Endodermis", "Metaphloem & Companion Cell","Protophloem", "Xylem", "Procambium","Xylem Pole Pericycle","Phloem Pole Pericycle", "Protoxylem", "Metaxylem", "Unknown")
palette <- c("#9400d3", "#DCD0FF","#5ab953", "#bfef45", "#008080", "#21B6A8", "#82b6ff", "#0000FF","#e6194b", "#dd77ec", "#9a6324", "#ffe119", "#ff9900", "#ffd4e3", "#9a6324", "#ddaa6f", "#EEEEEE")
rc.integrated$celltype.anno <- factor(rc.integrated$celltype.anno, levels = order[sort(match(unique(rc.integrated$celltype.anno),order))])
color <- palette[sort(match(unique(rc.integrated$celltype.anno),order))]
options(repr.plot.width=10, repr.plot.height=8)
DimPlot(rc.integrated, reduction = "umap", group.by = "celltype.anno", cols = color)+ggtitle("celltype.anno")
# Plot time
options(repr.plot.width=10, repr.plot.height=8)
DimPlot(rc.integrated, reduction = "umap", group.by = "time.anno",order = c("Distal Columella","Proximal Columella","Distal Lateral Root Cap","Proximal Lateral Root Cap","Maturation","Elongation","Meristem"),cols = c("#e5f5e0", "#a1d99b", "#31a354", "#deebf7", "#3182bd", '#fee0d2','#de2d26'))
table(rc.integrated$consensus.time.group)
T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 1278 808 1815 2840 2718 2574 2351 2041 3023 3152
options(repr.plot.width=5, repr.plot.height=4)
DimPlot(rc.integrated, reduction = "umap", group.by = "consensus.time.group", cols=brewer.pal(10,"Spectral"))
options(repr.plot.width=9, repr.plot.height=8)
DefaultAssay(rc.integrated) <- "integrated"
(SCR <- FeaturePlot(rc.integrated, features = "AT3G54220",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("SCR"))
options(repr.plot.width=9, repr.plot.height=8)
DefaultAssay(rc.integrated) <- "integrated"
FeaturePlot(rc.integrated, features = "AT1G17285",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("AT1G17285")
options(repr.plot.width=9, repr.plot.height=8)
DefaultAssay(rc.integrated) <- "integrated"
FeaturePlot(rc.integrated, features = "AT4G09760",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("AT4G09760")
options(repr.plot.width=9, repr.plot.height=8)
DefaultAssay(rc.integrated) <- "integrated"
FeaturePlot(rc.integrated, features = "AT5G57620",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("MYB36")
options(repr.plot.width=9, repr.plot.height=8)
DefaultAssay(rc.integrated) <- "integrated"
FeaturePlot(rc.integrated, features = "AT2G36100",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("CASP1")
options(repr.plot.width=9, repr.plot.height=8)
DefaultAssay(rc.integrated) <- "integrated"
FeaturePlot(rc.integrated, features = "AT1G09750",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("CORTEX")
options(repr.plot.width=9, repr.plot.height=8)
DefaultAssay(rc.integrated) <- "integrated"
FeaturePlot(rc.integrated, features = "AT5G07990",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("CYP75B1")
options(repr.plot.width=9, repr.plot.height=8)
DefaultAssay(rc.integrated) <- "integrated"
FeaturePlot(rc.integrated, features = "AT3G21670",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("NPF6.4")
# FindMarkers for celltype and time combination
rc.integrated$cell_group <- paste(rc.integrated$celltype.anno, rc.integrated$consensus.time.group, sep="_")
table(rc.integrated$cell_group)
Cortex_T0 Cortex_T1 Cortex_T2 Cortex_T3
591 329 493 1216
Cortex_T4 Cortex_T5 Cortex_T6 Cortex_T7
1315 1442 1446 1282
Cortex_T8 Cortex_T9 Endodermis_T0 Endodermis_T1
1757 1202 610 398
Endodermis_T2 Endodermis_T3 Endodermis_T4 Endodermis_T5
1322 1624 1403 1132
Endodermis_T6 Endodermis_T7 Endodermis_T8 Endodermis_T9
905 759 1266 1950
Quiescent Center_T0 Quiescent Center_T1
77 81
table(rc.integrated$celltype.anno, rc.integrated$consensus.time.group)
T0 T1 T2 T3 T4 T5 T6 T7 T8 T9
Quiescent Center 77 81 0 0 0 0 0 0 0 0
Cortex 591 329 493 1216 1315 1442 1446 1282 1757 1202
Endodermis 610 398 1322 1624 1403 1132 905 759 1266 1950
Idents(rc.integrated) <- "cell_group"
Clust_Markers <- FindAllMarkers(rc.integrated,
max.cells.per.ident = 5000,
only.pos=T,
test.use="roc")
Calculating cluster Cortex_T4 Calculating cluster Cortex_T6 Calculating cluster Endodermis_T5 Calculating cluster Endodermis_T6 Calculating cluster Cortex_T9 Calculating cluster Endodermis_T1 Calculating cluster Cortex_T5 Calculating cluster Endodermis_T3 Calculating cluster Endodermis_T8 Calculating cluster Cortex_T7 Calculating cluster Endodermis_T7 Calculating cluster Endodermis_T4 Calculating cluster Cortex_T8 Calculating cluster Endodermis_T2 Calculating cluster Cortex_T0 Calculating cluster Endodermis_T9 Calculating cluster Cortex_T3 Calculating cluster Cortex_T1 Calculating cluster Quiescent Center_T1 Calculating cluster Quiescent Center_T0 Calculating cluster Endodermis_T0 Calculating cluster Cortex_T2
feature_names <- read_tsv("./supp_data/features.tsv.gz", col_names = c("gene", "Name", "Type")) %>%
select(-Type) %>%
distinct()
── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── cols( gene = col_character(), Name = col_character(), Type = col_character() )
feature_names$Name[which(feature_names$gene == "AT1G09750")]="CORTEX"
Clust_Markers <- left_join(Clust_Markers, feature_names)
Joining, by = c("gene", "Name")
Clust_Markers %>% group_by(cluster) %>% tally()
| cluster | n |
|---|---|
| <fct> | <int> |
| Cortex_T4 | 519 |
| Cortex_T6 | 210 |
| Endodermis_T5 | 271 |
| Endodermis_T6 | 201 |
| Cortex_T9 | 464 |
| Endodermis_T1 | 1803 |
| Cortex_T5 | 435 |
| Endodermis_T3 | 483 |
| Endodermis_T8 | 769 |
| Cortex_T7 | 198 |
| Endodermis_T7 | 267 |
| Endodermis_T4 | 325 |
| Cortex_T8 | 405 |
| Endodermis_T2 | 777 |
| Cortex_T0 | 2771 |
| Endodermis_T9 | 836 |
| Cortex_T3 | 608 |
| Cortex_T1 | 1935 |
| Quiescent Center_T1 | 1785 |
| Quiescent Center_T0 | 2436 |
| Endodermis_T0 | 2514 |
| Cortex_T2 | 588 |
Clust_Markers %>% group_by(cluster) %>% top_n(1, myAUC)
| myAUC | avg_diff | power | pct.1 | pct.2 | cluster | celltype | stage | gene | Name | pct.diff | pct.diff_rank | avg_diff_rank | myAUC_rank | combined_rank | long_cor | abs_long_cor |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <fct> | <chr> | <fct> | <chr> | <chr> | <dbl> | <int> | <int> | <int> | <int> | <dbl> | <dbl> |
| 0.851 | 1.6098124 | 0.702 | 0.960 | 0.527 | Endodermis_T7 | Endodermis | T7 | AT3G06125 | AT3G06125 | 0.433 | 59 | 66 | 1 | 17 | 1.00000000 | 1.00000000 |
| 0.873 | 1.3599619 | 0.746 | 0.992 | 0.497 | Endodermis_T6 | Endodermis | T6 | AT1G02900 | RALF1 | 0.495 | 30 | 63 | 1 | 10 | 0.98787879 | 0.98787879 |
| 0.881 | 2.6551783 | 0.762 | 0.878 | 0.227 | Cortex_T2 | Cortex | T2 | AT5G14020 | AT5G14020 | 0.651 | 1 | 9 | 1 | 1 | -0.97575758 | 0.97575758 |
| 0.933 | 2.2197096 | 0.866 | 0.976 | 0.181 | Cortex_T8 | Cortex | T8 | AT5G15180 | PER56 | 0.795 | 1 | 36 | 1 | 1 | 0.95151515 | 0.95151515 |
| 0.959 | 2.5184213 | 0.918 | 0.996 | 0.201 | Cortex_T9 | Cortex | T9 | AT5G15180 | PER56 | 0.795 | 2 | 95 | 1 | 13 | 0.95151515 | 0.95151515 |
| 0.851 | 1.5120091 | 0.702 | 0.916 | 0.240 | Endodermis_T7 | Endodermis | T7 | AT5G66390 | PER72 | 0.676 | 1 | 75 | 2 | 6 | 0.92727273 | 0.92727273 |
| 0.866 | 1.5772820 | 0.732 | 0.934 | 0.337 | Cortex_T7 | Cortex | T7 | AT1G13930 | AT1G13930 | 0.597 | 3 | 35 | 1 | 2 | 0.87878788 | 0.87878788 |
| 0.979 | 3.6306420 | 0.958 | 1.000 | 0.132 | Endodermis_T0 | Endodermis | T0 | AT5G02450 | RPL36C | 0.868 | 140 | 28 | 1 | 6 | -0.87878788 | 0.87878788 |
| 0.952 | 2.7290143 | 0.904 | 0.977 | 0.119 | Endodermis_T1 | Endodermis | T1 | AT5G02960 | RPS23B | 0.858 | 4 | 448 | 3 | 107 | -0.87878788 | 0.87878788 |
| 0.979 | 3.3209090 | 0.958 | 1.000 | 0.111 | Endodermis_T0 | Endodermis | T0 | AT4G15000 | RPL27C | 0.889 | 55 | 95 | 2 | 3 | -0.79393939 | 0.79393939 |
| 0.970 | 2.8440779 | 0.940 | 1.000 | 0.096 | Cortex_T0 | Cortex | T0 | AT1G27400 | RPL17A | 0.904 | 12 | 175 | 1 | 4 | -0.78181818 | 0.78181818 |
| 0.952 | 3.1418255 | 0.904 | 0.962 | 0.106 | Endodermis_T1 | Endodermis | T1 | AT4G18730 | RPL11C | 0.856 | 7 | 228 | 2 | 25 | -0.78181818 | 0.78181818 |
| 0.952 | 3.2032964 | 0.904 | 0.965 | 0.109 | Endodermis_T1 | Endodermis | T1 | AT2G19730 | RPL28A | 0.856 | 6 | 202 | 1 | 20 | -0.76969697 | 0.76969697 |
| 0.952 | 3.1430591 | 0.904 | 0.988 | 0.125 | Cortex_T1 | Cortex | T1 | AT1G57660 | RPL21E | 0.863 | 21 | 57 | 1 | 1 | -0.70909091 | 0.70909091 |
| 0.972 | 3.4287747 | 0.944 | 0.983 | 0.122 | Endodermis_T9 | Endodermis | T9 | AT2G39430 | DIR9 | 0.861 | 1 | 71 | 1 | 4 | 0.70909091 | 0.70909091 |
| 0.915 | 2.1388130 | 0.830 | 0.943 | 0.219 | Endodermis_T3 | Endodermis | T3 | AT1G62480 | AT1G62480 | 0.724 | 1 | 7 | 1 | 1 | -0.61212121 | 0.61212121 |
| 0.915 | 2.3013423 | 0.830 | 0.983 | 0.382 | Endodermis_T2 | Endodermis | T2 | AT1G11580 | ATPMEPCRA | 0.601 | 31 | 41 | 1 | 7 | -0.61212121 | 0.61212121 |
| 0.867 | 1.6638362 | 0.734 | 0.954 | 0.345 | Cortex_T6 | Cortex | T6 | AT2G39010 | PIP2-6 | 0.609 | 2 | 10 | 1 | 1 | 0.58787879 | 0.58787879 |
| 0.901 | 1.9858252 | 0.802 | 0.959 | 0.287 | Endodermis_T4 | Endodermis | T4 | AT5G13910 | LEP | 0.672 | 2 | 4 | 1 | 1 | -0.35757576 | 0.35757576 |
| 0.990 | 4.0380846 | 0.980 | 1.000 | 0.073 | Quiescent Center_T0 | Quiescent Center | T0 | AT2G28900 | OEP161 | 0.927 | 5 | 40 | 1 | 2 | -0.32121212 | 0.32121212 |
| 0.927 | 0.3517676 | 0.854 | 0.844 | 0.115 | Endodermis_T8 | Endodermis | T8 | AT1G55610 | BRL1 | 0.729 | 4 | 711 | 1 | 169 | 0.13939394 | 0.13939394 |
| 0.886 | 1.8773184 | 0.772 | 0.955 | 0.295 | Cortex_T4 | Cortex | T4 | AT5G11420 | AT5G11420 | 0.660 | 2 | 25 | 1 | 1 | 0.09090909 | 0.09090909 |
| 0.884 | 1.8559454 | 0.768 | 0.945 | 0.292 | Cortex_T5 | Cortex | T5 | AT5G11420 | AT5G11420 | 0.653 | 2 | 21 | 1 | 3 | 0.09090909 | 0.09090909 |
| 0.995 | 5.6111516 | 0.990 | 0.975 | 0.025 | Quiescent Center_T1 | Quiescent Center | T1 | AT4G27520 | ENODL2 | 0.950 | 2 | 10 | 1 | 2 | -0.07878788 | 0.07878788 |
| 0.891 | 1.8751420 | 0.782 | 0.981 | 0.371 | Endodermis_T5 | Endodermis | T5 | AT4G16447 | AT4G16447 | 0.610 | 6 | 16 | 1 | 2 | -0.06666667 | 0.06666667 |
| 0.990 | 3.9083440 | 0.980 | 1.000 | 0.050 | Quiescent Center_T0 | Quiescent Center | T0 | AT5G10625 | FLP2 | 0.950 | 1 | 60 | 2 | 4 | -0.05454545 | 0.05454545 |
| 0.892 | 1.7467310 | 0.784 | 0.895 | 0.208 | Cortex_T3 | Cortex | T3 | AT4G15160 | AT4G15160 | 0.687 | 1 | 108 | 1 | 10 | -0.03030303 | 0.03030303 |
Clust_Markers <- separate(Clust_Markers, cluster, into=c("celltype", "stage"), sep="_", remove=F)
Clust_Markers <- mutate(Clust_Markers, pct.diff=pct.1-pct.2)
Clust_Markers <- arrange(Clust_Markers, desc(pct.diff)) %>%
group_by(cluster) %>%
mutate(pct.diff_rank=dplyr::row_number()) %>%
arrange(desc(avg_diff)) %>%
mutate(avg_diff_rank=dplyr::row_number()) %>%
arrange(desc(myAUC)) %>%
mutate(myAUC_rank=dplyr::row_number()) %>%
mutate(combined_rank_raw=(pct.diff_rank + avg_diff_rank + myAUC_rank)/3) %>%
arrange(combined_rank_raw) %>%
mutate(combined_rank=dplyr::row_number()) %>%
select(-combined_rank_raw) %>%
arrange(combined_rank)
Clust_Markers
| myAUC | avg_diff | power | pct.1 | pct.2 | cluster | celltype | stage | gene | Name | pct.diff | pct.diff_rank | avg_diff_rank | myAUC_rank | combined_rank | long_cor | abs_long_cor |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <fct> | <chr> | <chr> | <chr> | <chr> | <dbl> | <int> | <int> | <int> | <int> | <dbl> | <dbl> |
| 0.901 | 1.985825 | 0.802 | 0.959 | 0.287 | Endodermis_T4 | Endodermis | T4 | AT5G13910 | LEP | 0.672 | 2 | 4 | 1 | 1 | -0.357575758 | 0.357575758 |
| 0.915 | 2.138813 | 0.830 | 0.943 | 0.219 | Endodermis_T3 | Endodermis | T3 | AT1G62480 | AT1G62480 | 0.724 | 1 | 7 | 1 | 1 | -0.612121212 | 0.612121212 |
| 0.881 | 2.655178 | 0.762 | 0.878 | 0.227 | Cortex_T2 | Cortex | T2 | AT5G14020 | AT5G14020 | 0.651 | 1 | 9 | 1 | 1 | -0.975757576 | 0.975757576 |
| 0.993 | 5.784636 | 0.986 | 0.988 | 0.045 | Quiescent Center_T1 | Quiescent Center | T1 | AT2G41800 | AT2G41800 | 0.943 | 4 | 6 | 2 | 1 | -0.200000000 | 0.200000000 |
| 0.880 | 1.977404 | 0.760 | 0.927 | 0.253 | Cortex_T5 | Cortex | T5 | AT1G41830 | SKS6 | 0.674 | 1 | 9 | 2 | 1 | -0.175757576 | 0.175757576 |
| 0.867 | 1.663836 | 0.734 | 0.954 | 0.345 | Cortex_T6 | Cortex | T6 | AT2G39010 | PIP2-6 | 0.609 | 2 | 10 | 1 | 1 | 0.587878788 | 0.587878788 |
| 0.856 | 1.985059 | 0.712 | 0.940 | 0.330 | Endodermis_T5 | Endodermis | T5 | AT2G16700 | ADF5 | 0.610 | 7 | 8 | 7 | 1 | -0.006060606 | 0.006060606 |
| 0.935 | 3.109681 | 0.870 | 0.953 | 0.189 | Cortex_T9 | Cortex | T9 | AT5G44480 | DUR | 0.764 | 4 | 17 | 4 | 1 | 0.915151515 | 0.915151515 |
| 0.876 | 2.197686 | 0.752 | 0.910 | 0.311 | Cortex_T3 | Cortex | T3 | AT5G62210 | AT5G62210 | 0.599 | 7 | 15 | 3 | 1 | -0.709090909 | 0.709090909 |
| 0.886 | 1.877318 | 0.772 | 0.955 | 0.295 | Cortex_T4 | Cortex | T4 | AT5G11420 | AT5G11420 | 0.660 | 2 | 25 | 1 | 1 | 0.090909091 | 0.090909091 |
| 0.866 | 1.792225 | 0.732 | 0.965 | 0.378 | Endodermis_T6 | Endodermis | T6 | AT4G16447 | AT4G16447 | 0.587 | 4 | 24 | 2 | 1 | -0.066666667 | 0.066666667 |
| 0.904 | 2.565345 | 0.808 | 0.915 | 0.171 | Endodermis_T2 | Endodermis | T2 | AT3G23730 | XTH16 | 0.744 | 1 | 28 | 3 | 1 | -0.806060606 | 0.806060606 |
| 0.829 | 1.921177 | 0.658 | 0.761 | 0.217 | Cortex_T7 | Cortex | T7 | AT3G18200 | AT3G18200 | 0.544 | 14 | 12 | 10 | 1 | 0.903030303 | 0.903030303 |
| 0.984 | 4.137071 | 0.968 | 0.987 | 0.055 | Quiescent Center_T0 | Quiescent Center | T0 | AT3G60900 | FLA10 | 0.932 | 3 | 29 | 6 | 1 | -0.248484848 | 0.248484848 |
| 0.933 | 2.219710 | 0.866 | 0.976 | 0.181 | Cortex_T8 | Cortex | T8 | AT5G15180 | PER56 | 0.795 | 1 | 36 | 1 | 1 | 0.951515152 | 0.951515152 |
| 0.840 | 1.908193 | 0.680 | 0.900 | 0.337 | Endodermis_T7 | Endodermis | T7 | AT2G15340 | AT2G15340 | 0.563 | 7 | 37 | 4 | 1 | 0.903030303 | 0.903030303 |
| 0.843 | 2.688312 | 0.686 | 0.708 | 0.060 | Endodermis_T8 | Endodermis | T8 | AT1G13600 | AtbZIP58 | 0.648 | 14 | 15 | 25 | 1 | 0.648484848 | 0.648484848 |
| 0.967 | 5.279871 | 0.934 | 0.964 | 0.280 | Endodermis_T9 | Endodermis | T9 | AT1G02500 | SAM1 | 0.684 | 55 | 2 | 2 | 1 | 0.321212121 | 0.321212121 |
| 0.950 | 3.611536 | 0.900 | 0.960 | 0.122 | Endodermis_T1 | Endodermis | T1 | AT1G57660 | RPL21E | 0.838 | 26 | 39 | 5 | 1 | -0.709090909 | 0.709090909 |
| 0.952 | 3.143059 | 0.904 | 0.988 | 0.125 | Cortex_T1 | Cortex | T1 | AT1G57660 | RPL21E | 0.863 | 24 | 57 | 1 | 1 | -0.709090909 | 0.709090909 |
| 0.976 | 3.490443 | 0.952 | 1.000 | 0.105 | Endodermis_T0 | Endodermis | T0 | AT4G18100 | RPL32A | 0.895 | 36 | 46 | 8 | 1 | -0.660606061 | 0.660606061 |
| 0.969 | 2.904778 | 0.938 | 0.986 | 0.078 | Cortex_T0 | Cortex | T0 | AT2G20490 | NOP10 | 0.908 | 8 | 149 | 2 | 1 | -0.248484848 | 0.248484848 |
| 0.886 | 1.867908 | 0.772 | 0.958 | 0.272 | Endodermis_T4 | Endodermis | T4 | AT2G23560 | MES7 | 0.686 | 1 | 9 | 2 | 2 | 0.078787879 | 0.078787879 |
| 0.866 | 2.037492 | 0.732 | 0.924 | 0.293 | Cortex_T5 | Cortex | T5 | AT4G34260 | FUC95A | 0.631 | 3 | 3 | 6 | 2 | 0.272727273 | 0.272727273 |
| 0.995 | 5.611152 | 0.990 | 0.975 | 0.025 | Quiescent Center_T1 | Quiescent Center | T1 | AT4G27520 | ENODL2 | 0.950 | 2 | 10 | 1 | 2 | -0.078787879 | 0.078787879 |
| 0.910 | 2.130515 | 0.820 | 0.972 | 0.279 | Endodermis_T3 | Endodermis | T3 | AT5G13910 | LEP | 0.693 | 3 | 8 | 3 | 2 | -0.357575758 | 0.357575758 |
| 0.891 | 1.875142 | 0.782 | 0.981 | 0.371 | Endodermis_T5 | Endodermis | T5 | AT4G16447 | AT4G16447 | 0.610 | 6 | 16 | 1 | 2 | -0.066666667 | 0.066666667 |
| 0.847 | 2.965077 | 0.694 | 0.700 | 0.165 | Cortex_T2 | Cortex | T2 | AT2G45050 | GATA2 | 0.535 | 21 | 1 | 5 | 2 | -0.866666667 | 0.866666667 |
| 0.919 | 3.414707 | 0.838 | 0.939 | 0.252 | Cortex_T9 | Cortex | T9 | AT4G34180 | CYCLASE1 | 0.687 | 13 | 3 | 12 | 2 | 0.915151515 | 0.915151515 |
| 0.872 | 1.858140 | 0.744 | 0.901 | 0.249 | Cortex_T4 | Cortex | T4 | AT5G12940 | AT5G12940 | 0.652 | 3 | 28 | 3 | 2 | -0.466666667 | 0.466666667 |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| 0.291 | 0.9024948 | 0.418 | 0.090 | 0.381 | Cortex_T0 | Cortex | T0 | AT2G07678 | AT2G07678 | -0.291 | 2766 | 2370 | 2763 | 2742 | 0.91515152 | 0.91515152 |
| 0.707 | 0.2615472 | 0.414 | 0.592 | 0.199 | Cortex_T0 | Cortex | T0 | AT4G14840 | AT4G14840 | 0.393 | 2475 | 2766 | 2659 | 2743 | -0.60000000 | 0.60000000 |
| 0.705 | 0.6576205 | 0.410 | 0.530 | 0.199 | Cortex_T0 | Cortex | T0 | AT3G04130 | AT3G04130 | 0.331 | 2678 | 2532 | 2692 | 2744 | -0.52727273 | 0.52727273 |
| 0.707 | 0.4129214 | 0.414 | 0.538 | 0.164 | Cortex_T0 | Cortex | T0 | AT2G07644 | AT2G07644 | 0.374 | 2555 | 2693 | 2656 | 2745 | -0.27272727 | 0.27272727 |
| 0.704 | 0.4836549 | 0.408 | 0.572 | 0.194 | Cortex_T0 | Cortex | T0 | AT2G31890 | RAP | 0.378 | 2534 | 2654 | 2719 | 2746 | 0.21212121 | 0.21212121 |
| 0.717 | 0.3329135 | 0.434 | 0.687 | 0.355 | Cortex_T0 | Cortex | T0 | AT3G16640 | TCTP1 | 0.332 | 2674 | 2732 | 2504 | 2747 | -0.93939394 | 0.93939394 |
| 0.719 | 0.3841605 | 0.438 | 0.139 | 0.039 | Cortex_T0 | Cortex | T0 | AT1G69850 | NPF4.6 | 0.100 | 2758 | 2704 | 2465 | 2748 | 0.27272727 | 0.27272727 |
| 0.701 | 0.7826382 | 0.402 | 0.474 | 0.176 | Cortex_T0 | Cortex | T0 | AT4G37590 | NPY5 | 0.298 | 2718 | 2459 | 2758 | 2749 | -0.12727273 | 0.12727273 |
| 0.713 | 0.4579377 | 0.426 | 0.673 | 0.362 | Cortex_T0 | Cortex | T0 | AT5G48580 | FKBP15-2 | 0.311 | 2706 | 2666 | 2564 | 2750 | -0.93939394 | 0.93939394 |
| 0.717 | 0.2759030 | 0.434 | 0.631 | 0.304 | Cortex_T0 | Cortex | T0 | AT3G10220 | TFCB | 0.327 | 2683 | 2758 | 2505 | 2751 | -0.95151515 | 0.95151515 |
| 0.706 | 0.5790248 | 0.412 | 0.582 | 0.257 | Cortex_T0 | Cortex | T0 | AT3G57550 | AGK2 | 0.325 | 2689 | 2587 | 2671 | 2752 | -0.46666667 | 0.46666667 |
| 0.701 | 0.4747664 | 0.402 | 0.628 | 0.253 | Cortex_T0 | Cortex | T0 | AT3G04980 | AT3G04980 | 0.375 | 2547 | 2658 | 2761 | 2753 | -0.26060606 | 0.26060606 |
| 0.711 | 0.4291586 | 0.422 | 0.667 | 0.344 | Cortex_T0 | Cortex | T0 | AT5G51120 | PABN1 | 0.323 | 2691 | 2686 | 2596 | 2754 | -0.93939394 | 0.93939394 |
| 0.713 | 0.2543547 | 0.426 | 0.650 | 0.303 | Cortex_T0 | Cortex | T0 | AT5G64610 | HAM1 | 0.347 | 2639 | 2771 | 2566 | 2755 | -0.97575758 | 0.97575758 |
| 0.702 | 0.5002980 | 0.404 | 0.636 | 0.271 | Cortex_T0 | Cortex | T0 | AT3G21350 | MED6 | 0.365 | 2584 | 2648 | 2744 | 2756 | -0.95151515 | 0.95151515 |
| 0.714 | 0.3878292 | 0.428 | 0.486 | 0.217 | Cortex_T0 | Cortex | T0 | AT4G35905 | AT4G35905 | 0.269 | 2729 | 2702 | 2547 | 2757 | -0.95151515 | 0.95151515 |
| 0.707 | 0.4371539 | 0.414 | 0.604 | 0.268 | Cortex_T0 | Cortex | T0 | AT1G14510 | AL7 | 0.336 | 2670 | 2676 | 2654 | 2758 | -0.90303030 | 0.90303030 |
| 0.704 | 0.5037687 | 0.408 | 0.553 | 0.208 | Cortex_T0 | Cortex | T0 | AT1G30480 | DRT111 | 0.345 | 2643 | 2644 | 2718 | 2759 | -0.40606061 | 0.40606061 |
| 0.706 | 0.3248766 | 0.412 | 0.668 | 0.309 | Cortex_T0 | Cortex | T0 | AT1G09150 | AT1G09150 | 0.359 | 2604 | 2734 | 2674 | 2760 | -0.95151515 | 0.95151515 |
| 0.254 | 0.7479319 | 0.492 | 0.029 | 0.309 | Cortex_T0 | Cortex | T0 | AT3G10450 | SCPL7 | -0.280 | 2765 | 2480 | 2767 | 2761 | 0.29696970 | 0.29696970 |
| 0.702 | 0.2572413 | 0.404 | 0.487 | 0.101 | Cortex_T0 | Cortex | T0 | AT3G28150 | AXY4L | 0.386 | 2502 | 2769 | 2746 | 2762 | -0.43030303 | 0.43030303 |
| 0.708 | 0.3945001 | 0.416 | 0.506 | 0.178 | Cortex_T0 | Cortex | T0 | AT1G48030 | LPD1 | 0.328 | 2682 | 2700 | 2643 | 2763 | -0.15151515 | 0.15151515 |
| 0.702 | 0.5557036 | 0.404 | 0.694 | 0.376 | Cortex_T0 | Cortex | T0 | AT5G42190 | SKP1B | 0.318 | 2700 | 2606 | 2743 | 2764 | -0.91515152 | 0.91515152 |
| 0.704 | 0.5109657 | 0.408 | 0.584 | 0.282 | Cortex_T0 | Cortex | T0 | AT1G29340 | PUB17 | 0.302 | 2714 | 2638 | 2717 | 2765 | -0.07878788 | 0.07878788 |
| 0.261 | 0.6517756 | 0.478 | 0.081 | 0.400 | Cortex_T0 | Cortex | T0 | AT1G31170 | ATSRX | -0.319 | 2767 | 2537 | 2766 | 2766 | 0.80606061 | 0.80606061 |
| 0.702 | 0.4294830 | 0.404 | 0.599 | 0.313 | Cortex_T0 | Cortex | T0 | AT4G14420 | AT4G14420 | 0.286 | 2722 | 2683 | 2745 | 2767 | -0.93939394 | 0.93939394 |
| 0.288 | 0.5294175 | 0.424 | 0.074 | 0.259 | Cortex_T0 | Cortex | T0 | AT5G03180 | AT5G03180 | -0.185 | 2763 | 2629 | 2765 | 2768 | 0.84242424 | 0.84242424 |
| 0.111 | 0.4886949 | 0.778 | 0.049 | 0.566 | Cortex_T0 | Cortex | T0 | AT2G24040 | AT2G24040 | -0.517 | 2771 | 2653 | 2771 | 2769 | 0.24848485 | 0.24848485 |
| 0.704 | 0.3193795 | 0.408 | 0.489 | 0.237 | Cortex_T0 | Cortex | T0 | AT5G03140 | LECRK82 | 0.252 | 2739 | 2738 | 2720 | 2770 | -0.79393939 | 0.79393939 |
| 0.217 | 0.4240761 | 0.566 | 0.096 | 0.314 | Cortex_T0 | Cortex | T0 | AT2G45290 | TKL-2 | -0.218 | 2764 | 2687 | 2769 | 2771 | 0.43030303 | 0.43030303 |
filter(Clust_Markers, celltype %in% c("Cortex", "Endodermis") & myAUC>=0.75) %>%
group_by(celltype) %>%
tally()
| celltype | n |
|---|---|
| <chr> | <int> |
| Cortex | 4852 |
| Endodermis | 4925 |
filter(Clust_Markers, celltype %in% c("Cortex", "Endodermis") & myAUC>=0.75) %>%
group_by(cluster) %>%
tally()
| cluster | n |
|---|---|
| <fct> | <int> |
| Cortex_T4 | 253 |
| Cortex_T6 | 86 |
| Endodermis_T5 | 140 |
| Endodermis_T6 | 81 |
| Cortex_T9 | 270 |
| Endodermis_T1 | 1205 |
| Cortex_T5 | 214 |
| Endodermis_T3 | 253 |
| Endodermis_T8 | 380 |
| Cortex_T7 | 77 |
| Endodermis_T7 | 67 |
| Endodermis_T4 | 174 |
| Cortex_T8 | 196 |
| Endodermis_T2 | 399 |
| Cortex_T0 | 1961 |
| Endodermis_T9 | 467 |
| Cortex_T3 | 275 |
| Cortex_T1 | 1298 |
| Endodermis_T0 | 1759 |
| Cortex_T2 | 222 |
table(Clust_Markers$stage)
T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 7721 5523 1365 1091 844 706 411 465 1174 1300
Clust_Markers$stage <- factor(Clust_Markers$stage, levels=c("T0", "T1", "T2", "T3", "T4", "T5", "T6", "T7", "T8", "T9"))
# write markers with AUC 0.75 and above to a csv
# "Cortex", "Endodermis"
Clust_Markers_to_write <- filter(Clust_Markers, celltype %in% c("Cortex", "Endodermis") & myAUC>=0.75) %>% arrange(celltype) %>% arrange(stage) %>% arrange(combined_rank)
write.csv(Clust_Markers_to_write, "./supp_data/WT_Endodermis_Cortex_markers_AUC_0.75.csv", row.names=F)
number_de_genes <- filter(Clust_Markers, celltype %in% c("Cortex", "Endodermis") & myAUC>=0.75) %>%
group_by(cluster) %>%
tally() %>%
separate(cluster, into=c("celltype", "stage"), sep="_")
number_de_genes$stage <- factor(number_de_genes$stage, levels=c("T0", "T1", "T2", "T3", "T4", "T5", "T6", "T7", "T8", "T9"))
(number_de_genes <- arrange(number_de_genes, celltype) %>% arrange(stage) %>% rename("n_de_genes"=n))
write.csv(number_de_genes, "./supp_data/WT_Endodermis_Cortex_markers_AUC_0.75_n_DE.csv", row.names=F)
| celltype | stage | n_de_genes |
|---|---|---|
| <chr> | <fct> | <int> |
| Cortex | T0 | 1961 |
| Endodermis | T0 | 1759 |
| Cortex | T1 | 1298 |
| Endodermis | T1 | 1205 |
| Cortex | T2 | 222 |
| Endodermis | T2 | 399 |
| Cortex | T3 | 275 |
| Endodermis | T3 | 253 |
| Cortex | T4 | 253 |
| Endodermis | T4 | 174 |
| Cortex | T5 | 214 |
| Endodermis | T5 | 140 |
| Cortex | T6 | 86 |
| Endodermis | T6 | 81 |
| Cortex | T7 | 77 |
| Endodermis | T7 | 67 |
| Cortex | T8 | 196 |
| Endodermis | T8 | 380 |
| Cortex | T9 | 270 |
| Endodermis | T9 | 467 |
table(Clust_Markers$stage)
T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 7721 5523 1365 1091 844 706 411 465 1174 1300
Clust_Markers$stage <- factor(Clust_Markers$stage, levels=c("T0", "T1", "T2", "T3", "T4", "T5", "T6", "T7", "T8", "T9"))
rc.integrated$consensus.time.group <- factor(rc.integrated$consensus.time.group, levels=c("T0", "T1", "T2", "T3", "T4", "T5", "T6", "T7", "T8", "T9"))
Idents(rc.integrated) <- "consensus.time.group"
# pseudobulk of each stage
afm <- as.matrix(rc.integrated@assays$integrated@data)
pooled <- matrix(nrow=nrow(afm), ncol = 0)
for (i in unique(rc.integrated@meta.data$consensus.time.group)) {
m <- afm[,which(rc.integrated@meta.data$consensus.time.group==i)]
pooled <- cbind(pooled, rowSums(m)/ncol(m))
}
unique(rc.integrated@meta.data$consensus.time.group)
colnames(pooled) <- unique(rc.integrated@meta.data$consensus.time.group)
pooled_df <- as_tibble(pooled, rownames = "gene")
pooled_df_long <- pivot_longer(pooled_df, cols = 2:ncol(pooled_df), names_to = "stage", values_to = "expression")
long_order <- tibble(stage=paste("T", rep(0:9), sep=""),
order=rep(1:10))
long_order
| stage | order |
|---|---|
| <chr> | <int> |
| T0 | 1 |
| T1 | 2 |
| T2 | 3 |
| T3 | 4 |
| T4 | 5 |
| T5 | 6 |
| T6 | 7 |
| T7 | 8 |
| T8 | 9 |
| T9 | 10 |
(pooled_df_long <- left_join(pooled_df_long, long_order) %>%
arrange(order))
Joining, by = "stage"
| gene | stage | expression | order |
|---|---|---|---|
| <chr> | <chr> | <dbl> | <int> |
| AT1G05260 | T0 | -0.9756156 | 1 |
| AT3G59370 | T0 | -2.1390137 | 1 |
| AT2G36100 | T0 | -0.5732628 | 1 |
| AT1G12080 | T0 | -1.9192388 | 1 |
| AT1G12090 | T0 | -0.8453402 | 1 |
| AT4G11290 | T0 | -1.0448425 | 1 |
| AT5G42180 | T0 | -0.6208027 | 1 |
| AT5G66390 | T0 | -0.7698246 | 1 |
| AT2G32300 | T0 | -1.1660403 | 1 |
| AT2G02130 | T0 | -1.4222126 | 1 |
| AT3G11550 | T0 | -0.4656793 | 1 |
| AT4G35350 | T0 | -0.5410920 | 1 |
| AT1G30750 | T0 | -0.3857508 | 1 |
| AT4G40090 | T0 | -0.8454381 | 1 |
| AT1G20850 | T0 | -0.5737647 | 1 |
| AT2G39430 | T0 | -0.4500255 | 1 |
| AT1G75750 | T0 | -4.1100915 | 1 |
| AT4G13580 | T0 | -0.4837341 | 1 |
| AT4G25820 | T0 | -0.7139935 | 1 |
| AT4G23690 | T0 | -1.0530672 | 1 |
| AT1G26820 | T0 | -0.6452091 | 1 |
| AT5G64100 | T0 | -2.2258046 | 1 |
| AT1G65310 | T0 | -0.9921584 | 1 |
| AT2G40113 | T0 | -0.3543588 | 1 |
| AT5G17820 | T0 | -2.2810320 | 1 |
| AT3G24020 | T0 | -0.4305779 | 1 |
| AT5G04200 | T0 | -0.6187564 | 1 |
| AT3G54580 | T0 | -1.0985949 | 1 |
| AT3G09925 | T0 | -0.9476313 | 1 |
| AT5G46900 | T0 | -2.7217745 | 1 |
| ⋮ | ⋮ | ⋮ | ⋮ |
| AT4G22220 | T9 | -0.10157676 | 10 |
| AT2G23090 | T9 | 0.06355433 | 10 |
| AT2G46490 | T9 | -0.39573483 | 10 |
| AT3G27240 | T9 | 0.48059784 | 10 |
| AT1G07140 | T9 | 0.03226931 | 10 |
| AT1G76200 | T9 | 0.43662989 | 10 |
| AT5G08670 | T9 | 0.31597980 | 10 |
| AT1G04357 | T9 | -0.02525383 | 10 |
| AT1G64230 | T9 | 0.10779913 | 10 |
| AT2G02050 | T9 | 0.28476715 | 10 |
| AT3G09840 | T9 | 0.40582692 | 10 |
| AT5G47030 | T9 | 0.11472406 | 10 |
| AT1G10590 | T9 | -0.30711638 | 10 |
| AT1G08480 | T9 | 0.26458326 | 10 |
| AT5G61330 | T9 | 0.03782800 | 10 |
| AT4G02580 | T9 | -0.05323921 | 10 |
| AT5G08060 | T9 | 0.40793210 | 10 |
| AT1G75950 | T9 | -0.19641445 | 10 |
| AT2G20360 | T9 | 0.35039274 | 10 |
| AT4G30010 | T9 | 0.31325351 | 10 |
| AT4G06395 | T9 | -0.03931359 | 10 |
| AT3G55440 | T9 | 0.08067285 | 10 |
| AT3G03100 | T9 | 0.41172866 | 10 |
| AT5G54760 | T9 | -0.08012683 | 10 |
| AT2G33040 | T9 | 0.31443362 | 10 |
| AT2G42680 | T9 | 0.08661184 | 10 |
| AT5G11770 | T9 | 0.42159057 | 10 |
| AT5G08290 | T9 | -0.02513125 | 10 |
| AT5G53300 | T9 | 0.08732696 | 10 |
| AT5G64400 | T9 | 0.22821801 | 10 |
(long_corrs <- pooled_df_long %>%
group_by(gene) %>%
summarise(long_cor = cor(order, expression, method = "spearman")))
`summarise()` ungrouping output (override with `.groups` argument)
| gene | long_cor |
|---|---|
| <chr> | <dbl> |
| AT1G01010 | 0.72121212 |
| AT1G01020 | -0.33333333 |
| AT1G01030 | -0.26060606 |
| AT1G01040 | 0.73333333 |
| AT1G01050 | -0.91515152 |
| AT1G01070 | 0.20000000 |
| AT1G01080 | -0.04242424 |
| AT1G01090 | -0.87878788 |
| AT1G01100 | -0.91515152 |
| AT1G01110 | -0.62424242 |
| AT1G01120 | 0.98787879 |
| AT1G01130 | 0.18787879 |
| AT1G01160 | -0.50303030 |
| AT1G01170 | 0.16363636 |
| AT1G01180 | 0.86666667 |
| AT1G01200 | 0.46666667 |
| AT1G01210 | -0.26060606 |
| AT1G01220 | -0.92727273 |
| AT1G01225 | -0.56363636 |
| AT1G01230 | 0.11515152 |
| AT1G01240 | 0.76969697 |
| AT1G01260 | -0.91515152 |
| AT1G01290 | -0.63636364 |
| AT1G01300 | -0.83030303 |
| AT1G01310 | 0.84242424 |
| AT1G01320 | -0.05454545 |
| AT1G01340 | 0.96363636 |
| AT1G01350 | 0.47878788 |
| AT1G01360 | -0.56363636 |
| AT1G01370 | -0.61212121 |
| ⋮ | ⋮ |
| AT5G67320 | 0.09090909 |
| AT5G67330 | 0.90303030 |
| AT5G67340 | 0.98787879 |
| AT5G67360 | -0.51515152 |
| AT5G67370 | 0.36969697 |
| AT5G67380 | 0.50303030 |
| AT5G67385 | -0.32121212 |
| AT5G67390 | -0.64848485 |
| AT5G67400 | 0.72121212 |
| AT5G67410 | -0.81818182 |
| AT5G67420 | -0.04242424 |
| AT5G67440 | 0.33333333 |
| AT5G67450 | 0.50303030 |
| AT5G67460 | -0.17575758 |
| AT5G67470 | 0.24848485 |
| AT5G67488 | 0.16363636 |
| AT5G67500 | 0.78181818 |
| AT5G67510 | -0.20000000 |
| AT5G67520 | 0.83030303 |
| AT5G67530 | -0.58787879 |
| AT5G67540 | -0.80606061 |
| AT5G67560 | 0.91515152 |
| AT5G67570 | -0.87878788 |
| AT5G67580 | 0.68484848 |
| AT5G67590 | 1.00000000 |
| AT5G67600 | 0.58787879 |
| AT5G67610 | -0.27272727 |
| AT5G67620 | 0.66060606 |
| AT5G67630 | -0.12727273 |
| AT5G67640 | -0.12727273 |
Clust_Markers <- left_join(Clust_Markers, long_corrs) %>%
mutate(abs_long_cor=abs(long_cor)) %>%
arrange(-abs_long_cor)
Clust_Markers
Joining, by = c("gene", "long_cor")
| myAUC | avg_diff | power | pct.1 | pct.2 | cluster | celltype | stage | gene | Name | pct.diff | pct.diff_rank | avg_diff_rank | myAUC_rank | combined_rank | long_cor | abs_long_cor |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <fct> | <chr> | <fct> | <chr> | <chr> | <dbl> | <int> | <int> | <int> | <int> | <dbl> | <dbl> |
| 0.851 | 1.6098124 | 0.702 | 0.960 | 0.527 | Endodermis_T7 | Endodermis | T7 | AT3G06125 | AT3G06125 | 0.433 | 59 | 66 | 1 | 17 | 1 | 1 |
| 0.906 | 2.2766098 | 0.812 | 0.985 | 0.515 | Endodermis_T8 | Endodermis | T8 | AT3G06125 | AT3G06125 | 0.470 | 158 | 50 | 4 | 27 | 1 | 1 |
| 0.938 | 3.6469189 | 0.876 | 0.947 | 0.169 | Endodermis_T1 | Endodermis | T1 | AT2G31610 | RPS3A | 0.778 | 124 | 29 | 119 | 36 | -1 | 1 |
| 0.838 | 3.0433052 | 0.676 | 0.891 | 0.401 | Cortex_T9 | Cortex | T9 | AT1G11910 | APA1 | 0.490 | 117 | 20 | 77 | 45 | 1 | 1 |
| 0.890 | 4.6947655 | 0.780 | 0.900 | 0.340 | Endodermis_T9 | Endodermis | T9 | AT5G19590 | AT5G19590 | 0.560 | 164 | 8 | 72 | 47 | 1 | 1 |
| 0.932 | 4.8121159 | 0.864 | 0.971 | 0.507 | Endodermis_T9 | Endodermis | T9 | AT5G55850 | NOI | 0.464 | 298 | 7 | 30 | 57 | 1 | 1 |
| 0.770 | 1.1769976 | 0.540 | 0.850 | 0.414 | Endodermis_T6 | Endodermis | T6 | AT3G21240 | 4CL2 | 0.436 | 63 | 95 | 54 | 58 | 1 | 1 |
| 0.982 | 4.9356199 | 0.964 | 1.000 | 0.285 | Quiescent Center_T1 | Quiescent Center | T1 | AT5G65700 | BAM1 | 0.715 | 268 | 39 | 17 | 67 | -1 | 1 |
| 0.891 | 4.2146378 | 0.782 | 0.927 | 0.468 | Endodermis_T9 | Endodermis | T9 | AT3G61260 | AT3G61260 | 0.459 | 303 | 23 | 70 | 72 | 1 | 1 |
| 0.747 | 1.1724069 | 0.494 | 0.853 | 0.487 | Cortex_T7 | Cortex | T7 | AT4G39080 | VHA-A3 | 0.366 | 109 | 78 | 80 | 82 | 1 | 1 |
| 0.888 | 2.3030605 | 0.776 | 0.945 | 0.412 | Endodermis_T9 | Endodermis | T9 | AT2G37040 | PAL1 | 0.533 | 191 | 172 | 77 | 87 | 1 | 1 |
| 0.849 | 3.0011386 | 0.698 | 0.933 | 0.407 | Endodermis_T9 | Endodermis | T9 | AT4G22120 | CSC1 | 0.526 | 203 | 102 | 139 | 89 | 1 | 1 |
| 0.847 | 2.5222584 | 0.694 | 0.941 | 0.509 | Cortex_T9 | Cortex | T9 | AT5G43600 | UAH | 0.432 | 196 | 93 | 60 | 100 | 1 | 1 |
| 0.788 | 2.3322872 | 0.576 | 0.856 | 0.518 | Cortex_T8 | Cortex | T8 | AT1G05850 | CTL1 | 0.338 | 273 | 18 | 105 | 101 | 1 | 1 |
| 0.960 | 3.8584946 | 0.920 | 0.975 | 0.258 | Quiescent Center_T1 | Quiescent Center | T1 | AT1G14720 | XTH28 | 0.717 | 262 | 178 | 58 | 101 | -1 | 1 |
| 0.834 | 2.5700739 | 0.668 | 0.917 | 0.485 | Cortex_T9 | Cortex | T9 | AT4G39080 | VHA-A3 | 0.432 | 195 | 86 | 85 | 104 | 1 | 1 |
| 0.718 | 1.6598366 | 0.436 | 0.821 | 0.498 | Cortex_T7 | Cortex | T7 | AT5G34850 | PAP26 | 0.323 | 147 | 27 | 143 | 109 | 1 | 1 |
| 0.973 | 2.9487679 | 0.946 | 0.992 | 0.160 | Endodermis_T0 | Endodermis | T0 | AT2G31610 | RPS3A | 0.832 | 219 | 240 | 43 | 114 | -1 | 1 |
| 0.842 | 2.3633329 | 0.684 | 0.923 | 0.494 | Cortex_T9 | Cortex | T9 | AT5G34850 | PAP26 | 0.429 | 198 | 134 | 69 | 119 | 1 | 1 |
| 0.797 | 1.6292793 | 0.594 | 0.920 | 0.500 | Cortex_T8 | Cortex | T8 | AT5G43600 | UAH | 0.420 | 147 | 200 | 89 | 122 | 1 | 1 |
| 0.732 | 1.2048915 | 0.464 | 0.817 | 0.527 | Cortex_T7 | Cortex | T7 | AT1G05850 | CTL1 | 0.290 | 170 | 75 | 106 | 125 | 1 | 1 |
| 0.798 | 0.7774996 | 0.596 | 0.734 | 0.247 | Cortex_T2 | Cortex | T2 | AT5G02500 | MED37E | 0.487 | 55 | 416 | 46 | 125 | -1 | 1 |
| 0.828 | 2.0517490 | 0.656 | 0.945 | 0.472 | Cortex_T9 | Cortex | T9 | AT3G11780 | AT3G11780 | 0.473 | 139 | 200 | 97 | 128 | 1 | 1 |
| 0.866 | 1.2079462 | 0.732 | 0.830 | 0.174 | Endodermis_T9 | Endodermis | T9 | AT5G42460 | AT5G42460 | 0.656 | 71 | 388 | 114 | 129 | 1 | 1 |
| 0.793 | 3.3132389 | 0.586 | 0.784 | 0.281 | Endodermis_T9 | Endodermis | T9 | AT1G45160 | AT1G45160 | 0.503 | 236 | 76 | 270 | 132 | 1 | 1 |
| 0.737 | 0.9381952 | 0.474 | 0.893 | 0.615 | Endodermis_T6 | Endodermis | T6 | AT1G44170 | ALDH3H1 | 0.278 | 171 | 137 | 101 | 149 | 1 | 1 |
| 0.800 | 1.3280052 | 0.600 | 0.894 | 0.485 | Cortex_T8 | Cortex | T8 | AT5G34850 | PAP26 | 0.409 | 162 | 275 | 85 | 149 | 1 | 1 |
| 0.949 | 3.0583001 | 0.898 | 0.790 | 0.061 | Quiescent Center_T1 | Quiescent Center | T1 | AT5G23820 | ML3 | 0.729 | 230 | 416 | 84 | 151 | -1 | 1 |
| 0.946 | 2.4256048 | 0.892 | 0.985 | 0.171 | Cortex_T1 | Cortex | T1 | AT2G31610 | RPS3A | 0.814 | 121 | 514 | 55 | 152 | -1 | 1 |
| 0.715 | 0.8701974 | 0.430 | 0.847 | 0.514 | Cortex_T7 | Cortex | T7 | AT5G43600 | UAH | 0.333 | 141 | 123 | 151 | 154 | 1 | 1 |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| 0.779 | 2.1044479 | 0.558 | 0.341 | 0.039 | Endodermis_T0 | Endodermis | T0 | AT2G40200 | BHLH51 | 0.302 | 2387 | 983 | 1378 | 1615 | -0.006060606 | 0.006060606 |
| 0.719 | 1.6471551 | 0.438 | 0.701 | 0.047 | Quiescent Center_T0 | Quiescent Center | T0 | AT2G18500 | OFP7 | 0.654 | 968 | 1371 | 2196 | 1647 | 0.006060606 | 0.006060606 |
| 0.798 | 1.7031908 | 0.596 | 0.506 | 0.034 | Cortex_T0 | Cortex | T0 | AT2G40200 | BHLH51 | 0.472 | 2016 | 1504 | 1260 | 1667 | -0.006060606 | 0.006060606 |
| 0.814 | 0.7249876 | 0.628 | 0.766 | 0.178 | Quiescent Center_T0 | Quiescent Center | T0 | AT1G30520 | AAE14 | 0.588 | 1345 | 2033 | 1253 | 1687 | 0.006060606 | 0.006060606 |
| 0.721 | 0.7262378 | 0.442 | 0.544 | 0.108 | Cortex_T1 | Cortex | T1 | AT5G45740 | AT5G45740 | 0.436 | 1380 | 1692 | 1650 | 1727 | -0.006060606 | 0.006060606 |
| 0.702 | 0.5558862 | 0.404 | 0.617 | 0.245 | Quiescent Center_T1 | Quiescent Center | T1 | AT1G51560 | AT1G51560 | 0.372 | 1542 | 1607 | 1708 | 1740 | 0.006060606 | 0.006060606 |
| 0.710 | 3.0171315 | 0.420 | 0.241 | 0.024 | Endodermis_T0 | Endodermis | T0 | AT5G56460 | PBL16 | 0.217 | 2463 | 197 | 2331 | 1745 | 0.006060606 | 0.006060606 |
| 0.774 | 1.7804675 | 0.548 | 0.740 | 0.234 | Quiescent Center_T0 | Quiescent Center | T0 | AT4G04350 | EMB2369 | 0.506 | 1842 | 1283 | 1654 | 1757 | -0.006060606 | 0.006060606 |
| 0.704 | 3.4770447 | 0.408 | 0.416 | 0.039 | Quiescent Center_T0 | Quiescent Center | T0 | AT5G52870 | MAKR5 | 0.377 | 2260 | 182 | 2338 | 1758 | 0.006060606 | 0.006060606 |
| 0.773 | 1.7735576 | 0.546 | 0.633 | 0.174 | Cortex_T0 | Cortex | T0 | AT3G62310 | AT3G62310 | 0.459 | 2112 | 1404 | 1596 | 1796 | -0.006060606 | 0.006060606 |
| 0.710 | 1.3150559 | 0.420 | 0.666 | 0.383 | Cortex_T1 | Cortex | T1 | AT1G70310 | SPDSYN2 | 0.283 | 1896 | 1326 | 1790 | 1812 | -0.006060606 | 0.006060606 |
| 0.733 | 1.9598097 | 0.466 | 0.587 | 0.094 | Cortex_T0 | Cortex | T0 | AT2G43445 | AT2G43445 | 0.493 | 1844 | 1150 | 2208 | 1850 | 0.006060606 | 0.006060606 |
| 0.737 | 2.1951330 | 0.474 | 0.248 | 0.011 | Endodermis_T0 | Endodermis | T0 | AT1G21140 | AT1G21140 | 0.237 | 2446 | 862 | 1941 | 1854 | -0.006060606 | 0.006060606 |
| 0.752 | 1.3819277 | 0.504 | 0.552 | 0.128 | Endodermis_T0 | Endodermis | T0 | AT3G14580 | AT3G14580 | 0.424 | 1962 | 1700 | 1730 | 1910 | -0.006060606 | 0.006060606 |
| 0.736 | 2.1224751 | 0.472 | 0.479 | 0.067 | Cortex_T0 | Cortex | T0 | AT1G64110 | AT1G64110 | 0.412 | 2378 | 921 | 2166 | 1949 | 0.006060606 | 0.006060606 |
| 0.867 | 0.3160424 | 0.734 | 0.247 | 0.020 | Quiescent Center_T0 | Quiescent Center | T0 | AT3G50740 | UGT72E1 | 0.227 | 2358 | 2381 | 790 | 2061 | 0.006060606 | 0.006060606 |
| 0.714 | 2.1115780 | 0.428 | 0.519 | 0.080 | Cortex_T0 | Cortex | T0 | AT5G05740 | EGY2 | 0.439 | 2240 | 936 | 2534 | 2062 | 0.006060606 | 0.006060606 |
| 0.780 | 0.3488409 | 0.560 | 0.485 | 0.048 | Endodermis_T0 | Endodermis | T0 | AT4G33170 | PCMP-H53 | 0.437 | 1885 | 2476 | 1375 | 2065 | 0.006060606 | 0.006060606 |
| 0.748 | 1.2753085 | 0.496 | 0.597 | 0.091 | Cortex_T0 | Cortex | T0 | AT4G37380 | ELI1 | 0.506 | 1745 | 2019 | 1983 | 2079 | 0.006060606 | 0.006060606 |
| 0.731 | 1.7699078 | 0.462 | 0.236 | 0.068 | Endodermis_T0 | Endodermis | T0 | AT5G25170 | AT5G25170 | 0.168 | 2476 | 1318 | 2034 | 2107 | 0.006060606 | 0.006060606 |
| 0.284 | 2.1561160 | 0.432 | 0.049 | 0.179 | Endodermis_T0 | Endodermis | T0 | AT5G02420 | SMR3 | -0.130 | 2501 | 916 | 2507 | 2141 | -0.006060606 | 0.006060606 |
| 0.733 | 0.9584491 | 0.466 | 0.556 | 0.110 | Endodermis_T0 | Endodermis | T0 | AT1G56500 | SOQ1 | 0.446 | 1828 | 2100 | 2009 | 2146 | -0.006060606 | 0.006060606 |
| 0.781 | 0.5398159 | 0.562 | 0.569 | 0.075 | Cortex_T0 | Cortex | T0 | AT3G50840 | AT3G50840 | 0.494 | 1836 | 2620 | 1482 | 2156 | -0.006060606 | 0.006060606 |
| 0.766 | 1.3164257 | 0.532 | 0.783 | 0.377 | Cortex_T0 | Cortex | T0 | AT1G70310 | SPDSYN2 | 0.406 | 2410 | 1976 | 1713 | 2228 | -0.006060606 | 0.006060606 |
| 0.742 | 0.5649568 | 0.484 | 0.558 | 0.078 | Quiescent Center_T0 | Quiescent Center | T0 | AT1G14480 | AT1G14480 | 0.480 | 1948 | 2178 | 1960 | 2251 | -0.006060606 | 0.006060606 |
| 0.222 | 1.1516701 | 0.556 | 0.078 | 0.413 | Quiescent Center_T0 | Quiescent Center | T0 | AT1G28100 | AT1G28100 | -0.335 | 2434 | 1694 | 2433 | 2373 | -0.006060606 | 0.006060606 |
| 0.722 | 0.3498067 | 0.444 | 0.443 | 0.097 | Endodermis_T0 | Endodermis | T0 | AT5G54290 | CcdA | 0.346 | 2297 | 2475 | 2158 | 2448 | 0.006060606 | 0.006060606 |
| 0.754 | 0.8085993 | 0.508 | 0.536 | 0.173 | Cortex_T0 | Cortex | T0 | AT3G18370 | SYTF | 0.363 | 2590 | 2443 | 1889 | 2515 | -0.006060606 | 0.006060606 |
| 0.703 | 1.5358949 | 0.406 | 0.452 | 0.097 | Cortex_T0 | Cortex | T0 | AT5G54290 | CcdA | 0.355 | 2616 | 1704 | 2728 | 2547 | 0.006060606 | 0.006060606 |
| 0.735 | 0.6301417 | 0.470 | 0.225 | 0.016 | Cortex_T0 | Cortex | T0 | AT3G50740 | UGT72E1 | 0.209 | 2747 | 2551 | 2185 | 2661 | 0.006060606 | 0.006060606 |
genes_to_plt_df <- filter(Clust_Markers, celltype %in% c("Endodermis")) %>%
group_by(stage) %>%
top_n(20, -combined_rank) %>%
top_n(10, abs_long_cor) %>%
ungroup() %>%
arrange(stage)
# genes manually added to plotting list - these are known markers we want to make sure are there
to_add <- filter(Clust_Markers, celltype %in% c("Endodermis")) %>% filter(Name=="SCR" | Name=="MYB36" | Name=="CASP1")
(genes_to_plt_df <- bind_rows(genes_to_plt_df, to_add) %>%
ungroup() %>%
group_by(gene) %>%
top_n(1, -combined_rank) %>% # order genes by stage of highest rank
ungroup() %>% arrange(stage))
genes_to_plt <- unique(genes_to_plt_df$gene)
genes_to_plt_endo <- rev(genes_to_plt) # order to pointing upwards
| myAUC | avg_diff | power | pct.1 | pct.2 | cluster | celltype | stage | gene | Name | pct.diff | pct.diff_rank | avg_diff_rank | myAUC_rank | combined_rank | long_cor | abs_long_cor |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <fct> | <chr> | <fct> | <chr> | <chr> | <dbl> | <int> | <int> | <int> | <int> | <dbl> | <dbl> |
| 0.977 | 3.347157 | 0.954 | 0.997 | 0.116 | Endodermis_T0 | Endodermis | T0 | AT3G60245 | RPL37AC | 0.881 | 85 | 84 | 3 | 7 | -0.9151515 | 0.9151515 |
| 0.974 | 3.623934 | 0.948 | 0.997 | 0.126 | Endodermis_T0 | Endodermis | T0 | AT4G31700 | RPS6A | 0.871 | 129 | 30 | 26 | 11 | -0.9151515 | 0.9151515 |
| 0.975 | 3.270026 | 0.950 | 0.998 | 0.107 | Endodermis_T0 | Endodermis | T0 | AT3G56340 | RPS26C | 0.891 | 50 | 104 | 19 | 8 | -0.8909091 | 0.8909091 |
| 0.977 | 3.070570 | 0.954 | 1.000 | 0.097 | Endodermis_T0 | Endodermis | T0 | AT5G27850 | RPL18C | 0.903 | 15 | 176 | 6 | 13 | -0.8909091 | 0.8909091 |
| 0.977 | 3.254537 | 0.954 | 1.000 | 0.110 | Endodermis_T0 | Endodermis | T0 | AT5G02960 | RPS23B | 0.890 | 52 | 108 | 4 | 5 | -0.8787879 | 0.8787879 |
| 0.979 | 3.630642 | 0.958 | 1.000 | 0.132 | Endodermis_T0 | Endodermis | T0 | AT5G02450 | RPL36C | 0.868 | 142 | 28 | 1 | 6 | -0.8787879 | 0.8787879 |
| 0.975 | 3.364823 | 0.950 | 0.998 | 0.116 | Endodermis_T0 | Endodermis | T0 | AT1G70600 | RPL27AC | 0.882 | 81 | 79 | 18 | 9 | -0.8787879 | 0.8787879 |
| 0.971 | 3.621341 | 0.942 | 0.995 | 0.105 | Endodermis_T0 | Endodermis | T0 | AT2G27530 | RPL10AB | 0.890 | 53 | 31 | 64 | 2 | -0.8545455 | 0.8545455 |
| 0.977 | 3.224431 | 0.954 | 0.997 | 0.110 | Endodermis_T0 | Endodermis | T0 | AT3G11510 | RPS14B | 0.887 | 64 | 125 | 5 | 12 | -0.8303030 | 0.8303030 |
| 0.979 | 3.320909 | 0.958 | 1.000 | 0.111 | Endodermis_T0 | Endodermis | T0 | AT4G15000 | RPL27C | 0.889 | 56 | 95 | 2 | 3 | -0.7939394 | 0.7939394 |
| 0.975 | 3.103580 | 0.950 | 0.998 | 0.096 | Endodermis_T0 | Endodermis | T0 | AT4G16720 | RPL15A | 0.902 | 16 | 163 | 23 | 16 | -0.7939394 | 0.7939394 |
| 0.975 | 3.151219 | 0.950 | 1.000 | 0.105 | Endodermis_T0 | Endodermis | T0 | AT5G16130 | RPS7C | 0.895 | 35 | 151 | 21 | 17 | -0.7939394 | 0.7939394 |
| 0.950 | 3.353602 | 0.900 | 0.975 | 0.144 | Endodermis_T1 | Endodermis | T1 | AT3G62250 | RPS27AC | 0.831 | 36 | 131 | 7 | 10 | -0.9272727 | 0.9272727 |
| 0.948 | 3.404558 | 0.896 | 0.942 | 0.114 | Endodermis_T1 | Endodermis | T1 | AT5G23740 | RPS11C | 0.828 | 45 | 106 | 25 | 13 | -0.9272727 | 0.9272727 |
| 0.948 | 3.297031 | 0.896 | 0.960 | 0.118 | Endodermis_T1 | Endodermis | T1 | AT5G15200 | RPS9B | 0.842 | 21 | 155 | 27 | 18 | -0.9272727 | 0.9272727 |
| 0.950 | 3.392289 | 0.900 | 0.952 | 0.125 | Endodermis_T1 | Endodermis | T1 | AT3G09200 | RPP0B | 0.827 | 47 | 113 | 6 | 7 | -0.9151515 | 0.9151515 |
| 0.951 | 3.355050 | 0.902 | 0.955 | 0.123 | Endodermis_T1 | Endodermis | T1 | AT1G72370 | RPSAA | 0.832 | 34 | 130 | 4 | 8 | -0.8909091 | 0.8909091 |
| 0.949 | 3.288305 | 0.898 | 0.955 | 0.122 | Endodermis_T1 | Endodermis | T1 | AT4G17390 | RPL15B | 0.833 | 31 | 157 | 17 | 19 | -0.8909091 | 0.8909091 |
| 0.949 | 3.416840 | 0.898 | 0.950 | 0.127 | Endodermis_T1 | Endodermis | T1 | AT3G55750 | RPL35AD | 0.823 | 57 | 102 | 14 | 9 | -0.8424242 | 0.8424242 |
| 0.945 | 3.537856 | 0.890 | 0.947 | 0.126 | Endodermis_T1 | Endodermis | T1 | AT1G09590 | RPL21A | 0.821 | 60 | 58 | 56 | 12 | -0.8424242 | 0.8424242 |
| 0.946 | 3.492686 | 0.892 | 0.930 | 0.116 | Endodermis_T1 | Endodermis | T1 | AT2G44120 | AT2G44120 | 0.814 | 72 | 74 | 47 | 16 | -0.8424242 | 0.8424242 |
| 0.949 | 3.351448 | 0.898 | 0.950 | 0.124 | Endodermis_T1 | Endodermis | T1 | AT3G23390 | RPL36AB | 0.826 | 51 | 132 | 16 | 17 | -0.8424242 | 0.8424242 |
| 0.882 | 2.216631 | 0.764 | 0.960 | 0.338 | Endodermis_T2 | Endodermis | T2 | AT4G16265 | NRPB9B | 0.622 | 19 | 48 | 8 | 9 | -0.9393939 | 0.9393939 |
| 0.871 | 2.125290 | 0.742 | 0.955 | 0.412 | Endodermis_T2 | Endodermis | T2 | AT2G05990 | MOD1 | 0.543 | 69 | 53 | 12 | 18 | -0.9393939 | 0.9393939 |
| 0.868 | 2.323972 | 0.736 | 0.938 | 0.357 | Endodermis_T2 | Endodermis | T2 | AT2G30200 | AT2G30200 | 0.581 | 40 | 38 | 16 | 10 | -0.9151515 | 0.9151515 |
| 0.892 | 2.720810 | 0.784 | 0.955 | 0.428 | Endodermis_T2 | Endodermis | T2 | AT1G54580 | ACP2 | 0.527 | 90 | 17 | 6 | 16 | -0.9030303 | 0.9030303 |
| 0.849 | 2.256817 | 0.698 | 0.884 | 0.274 | Endodermis_T2 | Endodermis | T2 | AT2G43360 | BIO2 | 0.610 | 25 | 45 | 35 | 15 | -0.8909091 | 0.8909091 |
| 0.847 | 2.385227 | 0.694 | 0.899 | 0.336 | Endodermis_T2 | Endodermis | T2 | AT4G39900 | AT4G39900 | 0.563 | 57 | 33 | 37 | 17 | -0.8909091 | 0.8909091 |
| 0.831 | 2.315298 | 0.662 | 0.722 | 0.124 | Endodermis_T2 | Endodermis | T2 | AT5G07030 | AT5G07030 | 0.598 | 32 | 39 | 73 | 20 | -0.8666667 | 0.8666667 |
| 0.893 | 2.446549 | 0.786 | 0.922 | 0.251 | Endodermis_T2 | Endodermis | T2 | AT5G55730 | FLA1 | 0.671 | 5 | 31 | 5 | 2 | -0.8545455 | 0.8545455 |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| 0.822 | 1.576349 | 0.644 | 0.797 | 0.210 | Endodermis_T6 | Endodermis | T6 | AT4G15960 | AT4G15960 | 0.587 | 2 | 41 | 11 | 2 | 0.63636364 | 0.63636364 |
| 0.817 | 1.069673 | 0.634 | 0.970 | 0.427 | Endodermis_T6 | Endodermis | T6 | AT5G57620 | MYB36 | 0.543 | 12 | 111 | 14 | 26 | 0.01818182 | 0.01818182 |
| 0.851 | 1.609812 | 0.702 | 0.960 | 0.527 | Endodermis_T7 | Endodermis | T7 | AT3G06125 | AT3G06125 | 0.433 | 59 | 66 | 1 | 17 | 1.00000000 | 1.00000000 |
| 0.849 | 1.305687 | 0.698 | 0.975 | 0.396 | Endodermis_T7 | Endodermis | T7 | AT1G61590 | PBL15 | 0.579 | 4 | 103 | 3 | 12 | 0.98787879 | 0.98787879 |
| 0.806 | 1.661355 | 0.612 | 0.913 | 0.457 | Endodermis_T7 | Endodermis | T7 | AT3G09270 | GSTU8 | 0.456 | 44 | 60 | 15 | 15 | 0.97575758 | 0.97575758 |
| 0.851 | 1.512009 | 0.702 | 0.916 | 0.240 | Endodermis_T7 | Endodermis | T7 | AT5G66390 | PER72 | 0.676 | 1 | 75 | 2 | 6 | 0.92727273 | 0.92727273 |
| 0.782 | 1.656955 | 0.564 | 0.819 | 0.316 | Endodermis_T7 | Endodermis | T7 | AT4G23493 | AT4G23493 | 0.503 | 17 | 62 | 23 | 11 | 0.91515152 | 0.91515152 |
| 0.840 | 1.908193 | 0.680 | 0.900 | 0.337 | Endodermis_T7 | Endodermis | T7 | AT2G15340 | AT2G15340 | 0.563 | 7 | 37 | 4 | 1 | 0.90303030 | 0.90303030 |
| 0.835 | 1.482905 | 0.670 | 0.934 | 0.365 | Endodermis_T7 | Endodermis | T7 | AT1G35260 | MLP165 | 0.569 | 6 | 81 | 8 | 10 | 0.90303030 | 0.90303030 |
| 0.819 | 2.007340 | 0.638 | 0.814 | 0.330 | Endodermis_T7 | Endodermis | T7 | AT4G34230 | CAD5 | 0.484 | 27 | 29 | 10 | 3 | 0.89090909 | 0.89090909 |
| 0.813 | 1.967599 | 0.626 | 0.698 | 0.139 | Endodermis_T7 | Endodermis | T7 | AT4G21620 | AT4G21620 | 0.559 | 8 | 32 | 11 | 2 | 0.85454545 | 0.85454545 |
| 0.810 | 1.917405 | 0.620 | 0.718 | 0.225 | Endodermis_T7 | Endodermis | T7 | AT4G37790 | HAT22 | 0.493 | 23 | 36 | 13 | 5 | 0.84242424 | 0.84242424 |
| 0.840 | 1.947747 | 0.680 | 0.831 | 0.191 | Endodermis_T8 | Endodermis | T8 | AT3G03520 | NPC3 | 0.640 | 16 | 98 | 31 | 18 | 0.91515152 | 0.91515152 |
| 0.837 | 2.677446 | 0.674 | 0.700 | 0.142 | Endodermis_T8 | Endodermis | T8 | AT1G03850 | AT1G03850 | 0.558 | 40 | 16 | 39 | 4 | 0.89090909 | 0.89090909 |
| 0.843 | 2.014614 | 0.686 | 0.862 | 0.184 | Endodermis_T8 | Endodermis | T8 | AT4G13580 | DIR18 | 0.678 | 11 | 85 | 26 | 13 | 0.87878788 | 0.87878788 |
| 0.839 | 2.596713 | 0.678 | 0.675 | 0.093 | Endodermis_T8 | Endodermis | T8 | AT3G05937 | AT3G05937 | 0.582 | 25 | 18 | 36 | 2 | 0.84242424 | 0.84242424 |
| 0.823 | 2.419715 | 0.646 | 0.730 | 0.167 | Endodermis_T8 | Endodermis | T8 | AT3G14280 | AT3G14280 | 0.563 | 36 | 30 | 66 | 17 | 0.83030303 | 0.83030303 |
| 0.851 | 2.157207 | 0.702 | 0.780 | 0.229 | Endodermis_T8 | Endodermis | T8 | AT5G08240 | AT5G08240 | 0.551 | 48 | 66 | 17 | 15 | 0.78181818 | 0.78181818 |
| 0.921 | 1.955217 | 0.842 | 0.987 | 0.224 | Endodermis_T8 | Endodermis | T8 | AT2G36100 | CASP1 | 0.763 | 2 | 95 | 2 | 6 | 0.74545455 | 0.74545455 |
| 0.966 | 3.437321 | 0.932 | 0.976 | 0.196 | Endodermis_T9 | Endodermis | T9 | AT2G27370 | CASP3 | 0.780 | 20 | 69 | 3 | 7 | 0.98787879 | 0.98787879 |
| 0.956 | 3.540249 | 0.912 | 0.967 | 0.292 | Endodermis_T9 | Endodermis | T9 | AT4G34050 | CCoAOMT1 | 0.675 | 61 | 64 | 6 | 13 | 0.98787879 | 0.98787879 |
| 0.909 | 4.324263 | 0.818 | 0.912 | 0.269 | Endodermis_T9 | Endodermis | T9 | AT5G44790 | RAN1 | 0.643 | 85 | 17 | 47 | 20 | 0.98787879 | 0.98787879 |
| 0.963 | 3.575249 | 0.926 | 0.968 | 0.129 | Endodermis_T9 | Endodermis | T9 | AT1G44970 | PER9 | 0.839 | 6 | 60 | 4 | 2 | 0.95151515 | 0.95151515 |
| 0.954 | 3.021530 | 0.908 | 0.969 | 0.135 | Endodermis_T9 | Endodermis | T9 | AT2G28671 | AT2G28671 | 0.834 | 7 | 98 | 9 | 8 | 0.91515152 | 0.91515152 |
| 0.937 | 3.624695 | 0.874 | 0.933 | 0.203 | Endodermis_T9 | Endodermis | T9 | AT5G65020 | ANN2 | 0.730 | 35 | 58 | 26 | 10 | 0.90303030 | 0.90303030 |
| 0.955 | 3.380457 | 0.910 | 0.965 | 0.104 | Endodermis_T9 | Endodermis | T9 | AT5G06200 | CASP4 | 0.861 | 1 | 74 | 7 | 5 | 0.73333333 | 0.73333333 |
| 0.972 | 3.428775 | 0.944 | 0.983 | 0.122 | Endodermis_T9 | Endodermis | T9 | AT2G39430 | DIR9 | 0.861 | 2 | 71 | 1 | 4 | 0.70909091 | 0.70909091 |
| 0.948 | 3.028116 | 0.896 | 0.963 | 0.115 | Endodermis_T9 | Endodermis | T9 | AT3G11550 | CASP2 | 0.848 | 3 | 97 | 14 | 9 | 0.69696970 | 0.69696970 |
| 0.924 | 3.250986 | 0.848 | 0.931 | 0.100 | Endodermis_T9 | Endodermis | T9 | AT1G71740 | AT1G71740 | 0.831 | 8 | 82 | 38 | 12 | 0.69696970 | 0.69696970 |
| 0.893 | 3.759473 | 0.786 | 0.887 | 0.112 | Endodermis_T9 | Endodermis | T9 | AT2G15300 | AT2G15300 | 0.775 | 22 | 49 | 69 | 17 | 0.69696970 | 0.69696970 |
genes_to_plt_df <- filter(Clust_Markers, celltype %in% c("Cortex")) %>%
group_by(stage) %>%
top_n(20, -combined_rank) %>%
top_n(10, abs_long_cor) %>%
ungroup() %>%
arrange(stage)
# to add AT4G09760 AT5G02000
to_add <- filter(Clust_Markers, celltype %in% c("Cortex")) %>% filter(gene %in% c("AT1G09750","AT5G07990","AT3G21670","AT4G09760", "AT5G02000", "AT5G64620"))
(genes_to_plt_df <- bind_rows(genes_to_plt_df, to_add) %>%
ungroup() %>%
group_by(gene) %>%
top_n(1, -combined_rank) %>%
ungroup() %>% arrange(stage))
(genes_to_plt_df <- genes_to_plt_df %>%
ungroup() %>%
group_by(gene) %>%
top_n(1, -combined_rank) %>%
ungroup() %>% arrange(stage))
genes_to_plt <- unique(genes_to_plt_df$gene)
genes_to_plt_cortex <- genes_to_plt
| myAUC | avg_diff | power | pct.1 | pct.2 | cluster | celltype | stage | gene | Name | pct.diff | pct.diff_rank | avg_diff_rank | myAUC_rank | combined_rank | long_cor | abs_long_cor |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <fct> | <chr> | <fct> | <chr> | <chr> | <dbl> | <int> | <int> | <int> | <int> | <dbl> | <dbl> |
| 0.962 | 2.841572 | 0.924 | 0.988 | 0.117 | Cortex_T0 | Cortex | T0 | AT5G28060 | RPS24B | 0.871 | 115 | 178 | 47 | 9 | -0.8787879 | 0.8787879 |
| 0.967 | 2.712818 | 0.934 | 1.000 | 0.136 | Cortex_T0 | Cortex | T0 | AT2G27720 | AT2G27720 | 0.864 | 135 | 269 | 5 | 13 | -0.8787879 | 0.8787879 |
| 0.964 | 2.682942 | 0.928 | 0.998 | 0.124 | Cortex_T0 | Cortex | T0 | AT3G02080 | RPS19A | 0.874 | 102 | 302 | 19 | 14 | -0.8303030 | 0.8303030 |
| 0.965 | 2.616760 | 0.930 | 0.997 | 0.106 | Cortex_T0 | Cortex | T0 | AT5G16130 | RPS7C | 0.891 | 39 | 345 | 14 | 12 | -0.7939394 | 0.7939394 |
| 0.970 | 2.844078 | 0.940 | 1.000 | 0.096 | Cortex_T0 | Cortex | T0 | AT1G27400 | RPL17A | 0.904 | 12 | 175 | 1 | 4 | -0.7818182 | 0.7818182 |
| 0.966 | 2.603655 | 0.932 | 1.000 | 0.096 | Cortex_T0 | Cortex | T0 | AT5G45775 | RPL11C | 0.904 | 13 | 353 | 9 | 11 | -0.7818182 | 0.7818182 |
| 0.967 | 2.697931 | 0.934 | 1.000 | 0.102 | Cortex_T0 | Cortex | T0 | AT3G16080 | RPL37C | 0.898 | 25 | 284 | 6 | 7 | -0.7090909 | 0.7090909 |
| 0.967 | 2.694637 | 0.934 | 0.998 | 0.093 | Cortex_T0 | Cortex | T0 | AT3G45030 | RPS20C | 0.905 | 11 | 287 | 7 | 6 | -0.6242424 | 0.6242424 |
| 0.965 | 2.575404 | 0.930 | 0.990 | 0.105 | Cortex_T0 | Cortex | T0 | AT3G62530 | AT3G62530 | 0.885 | 65 | 391 | 15 | 17 | -0.5878788 | 0.5878788 |
| 0.956 | 2.843506 | 0.912 | 0.971 | 0.114 | Cortex_T0 | Cortex | T0 | AT3G13580 | RPL7D | 0.857 | 158 | 176 | 147 | 20 | -0.5636364 | 0.5636364 |
| 0.949 | 2.995861 | 0.898 | 0.970 | 0.119 | Cortex_T1 | Cortex | T1 | AT2G01250 | RPL7B | 0.851 | 42 | 129 | 15 | 5 | -0.9272727 | 0.9272727 |
| 0.948 | 3.017097 | 0.896 | 0.964 | 0.117 | Cortex_T1 | Cortex | T1 | AT5G23740 | RPS11C | 0.847 | 54 | 117 | 24 | 6 | -0.9272727 | 0.9272727 |
| 0.950 | 2.797067 | 0.900 | 0.988 | 0.120 | Cortex_T1 | Cortex | T1 | AT5G15200 | RPS9B | 0.868 | 15 | 240 | 6 | 17 | -0.9272727 | 0.9272727 |
| 0.947 | 2.813544 | 0.894 | 0.985 | 0.119 | Cortex_T1 | Cortex | T1 | AT4G27090 | RPL14B | 0.866 | 18 | 227 | 38 | 18 | -0.9151515 | 0.9151515 |
| 0.949 | 2.975505 | 0.898 | 0.964 | 0.127 | Cortex_T1 | Cortex | T1 | AT1G56045 | RPL41G | 0.837 | 74 | 139 | 16 | 10 | -0.8909091 | 0.8909091 |
| 0.951 | 2.812709 | 0.902 | 0.988 | 0.109 | Cortex_T1 | Cortex | T1 | AT5G27850 | RPL18C | 0.879 | 4 | 228 | 2 | 12 | -0.8909091 | 0.8909091 |
| 0.947 | 2.950026 | 0.894 | 0.979 | 0.128 | Cortex_T1 | Cortex | T1 | AT3G02560 | RPS7B | 0.851 | 44 | 157 | 36 | 13 | -0.8909091 | 0.8909091 |
| 0.951 | 2.775165 | 0.902 | 0.988 | 0.125 | Cortex_T1 | Cortex | T1 | AT3G25520 | ATL5 | 0.863 | 21 | 264 | 3 | 20 | -0.8909091 | 0.8909091 |
| 0.947 | 2.970321 | 0.894 | 0.970 | 0.118 | Cortex_T1 | Cortex | T1 | AT1G22780 | RPS18C | 0.852 | 38 | 143 | 35 | 8 | -0.8787879 | 0.8787879 |
| 0.949 | 2.926049 | 0.898 | 0.976 | 0.125 | Cortex_T1 | Cortex | T1 | AT5G58420 | RPS4D | 0.851 | 47 | 164 | 17 | 9 | -0.8787879 | 0.8787879 |
| 0.857 | 2.403694 | 0.714 | 0.830 | 0.247 | Cortex_T2 | Cortex | T2 | AT1G17285 | AT1G17285 | 0.583 | 7 | 24 | 3 | 4 | -0.9878788 | 0.9878788 |
| 0.881 | 2.655178 | 0.762 | 0.878 | 0.227 | Cortex_T2 | Cortex | T2 | AT5G14020 | AT5G14020 | 0.651 | 1 | 9 | 1 | 1 | -0.9757576 | 0.9757576 |
| 0.809 | 2.229940 | 0.618 | 0.793 | 0.256 | Cortex_T2 | Cortex | T2 | AT2G24280 | AT2G24280 | 0.537 | 20 | 41 | 34 | 13 | -0.9757576 | 0.9757576 |
| 0.840 | 2.225051 | 0.680 | 0.710 | 0.165 | Cortex_T2 | Cortex | T2 | AT1G54000 | GLL22 | 0.545 | 18 | 42 | 10 | 9 | -0.9636364 | 0.9636364 |
| 0.831 | 1.791538 | 0.662 | 0.815 | 0.224 | Cortex_T2 | Cortex | T2 | AT1G32190 | AT1G32190 | 0.591 | 5 | 95 | 15 | 16 | -0.9393939 | 0.9393939 |
| 0.844 | 2.812988 | 0.688 | 0.886 | 0.406 | Cortex_T2 | Cortex | T2 | AT3G19820 | DIM | 0.480 | 66 | 5 | 6 | 11 | -0.9151515 | 0.9151515 |
| 0.843 | 1.745310 | 0.686 | 0.862 | 0.230 | Cortex_T2 | Cortex | T2 | AT1G26945 | PRE6 | 0.632 | 2 | 105 | 7 | 15 | -0.9151515 | 0.9151515 |
| 0.788 | 2.641667 | 0.576 | 0.710 | 0.211 | Cortex_T2 | Cortex | T2 | AT1G62810 | AT1G62810 | 0.499 | 43 | 10 | 72 | 18 | -0.9030303 | 0.9030303 |
| 0.847 | 2.965077 | 0.694 | 0.700 | 0.165 | Cortex_T2 | Cortex | T2 | AT2G45050 | GATA2 | 0.535 | 21 | 1 | 5 | 2 | -0.8666667 | 0.8666667 |
| 0.827 | 2.357117 | 0.654 | 0.688 | 0.164 | Cortex_T2 | Cortex | T2 | AT2G20515 | AT2G20515 | 0.524 | 29 | 27 | 17 | 10 | -0.8666667 | 0.8666667 |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| 0.867 | 1.663836 | 0.734 | 0.954 | 0.345 | Cortex_T6 | Cortex | T6 | AT2G39010 | PIP2-6 | 0.609 | 2 | 10 | 1 | 1 | 0.5878788 | 0.5878788 |
| 0.823 | 1.463082 | 0.646 | 0.914 | 0.343 | Cortex_T6 | Cortex | T6 | AT5G64620 | C/VIF2 | 0.571 | 6 | 26 | 11 | 2 | 0.5151515 | 0.5151515 |
| 0.808 | 1.655623 | 0.616 | 0.905 | 0.403 | Cortex_T6 | Cortex | T6 | AT5G66920 | sks17 | 0.502 | 19 | 13 | 16 | 4 | 0.5151515 | 0.5151515 |
| 0.823 | 1.463082 | 0.646 | 0.914 | 0.343 | Cortex_T6 | Cortex | T6 | AT5G64620 | C/VIF2 | 0.571 | 6 | 26 | 11 | 2 | 0.5151515 | 0.5151515 |
| 0.703 | 1.040975 | 0.406 | 0.734 | 0.282 | Cortex_T6 | Cortex | T6 | AT3G21670 | NPF6.4 | 0.452 | 51 | 96 | 198 | 121 | 0.4909091 | 0.4909091 |
| 0.816 | 1.464443 | 0.632 | 0.842 | 0.272 | Cortex_T7 | Cortex | T7 | AT4G25830 | AT4G25830 | 0.570 | 6 | 44 | 17 | 6 | 0.9515152 | 0.9515152 |
| 0.848 | 1.151143 | 0.696 | 0.977 | 0.382 | Cortex_T7 | Cortex | T7 | AT3G57020 | SSL9 | 0.595 | 4 | 80 | 4 | 11 | 0.9515152 | 0.9515152 |
| 0.835 | 1.257908 | 0.670 | 0.915 | 0.393 | Cortex_T7 | Cortex | T7 | AT4G23400 | PIP1-5 | 0.522 | 18 | 70 | 8 | 12 | 0.9515152 | 0.9515152 |
| 0.790 | 1.334410 | 0.580 | 0.793 | 0.276 | Cortex_T7 | Cortex | T7 | AT4G02700 | SULTR3;2 | 0.517 | 19 | 58 | 34 | 20 | 0.9393939 | 0.9393939 |
| 0.816 | 1.726037 | 0.632 | 0.746 | 0.202 | Cortex_T7 | Cortex | T7 | AT4G00330 | CRCK2 | 0.544 | 13 | 21 | 16 | 3 | 0.9272727 | 0.9272727 |
| 0.829 | 1.136766 | 0.658 | 0.937 | 0.376 | Cortex_T7 | Cortex | T7 | AT3G14690 | CYP72A15 | 0.561 | 7 | 82 | 11 | 15 | 0.9272727 | 0.9272727 |
| 0.804 | 1.752173 | 0.608 | 0.720 | 0.175 | Cortex_T7 | Cortex | T7 | AT5G25810 | TINY | 0.545 | 12 | 18 | 27 | 5 | 0.9151515 | 0.9151515 |
| 0.793 | 1.969611 | 0.586 | 0.666 | 0.202 | Cortex_T7 | Cortex | T7 | AT1G66725 | MIR163 | 0.464 | 37 | 10 | 33 | 10 | 0.9151515 | 0.9151515 |
| 0.863 | 2.411867 | 0.726 | 0.777 | 0.192 | Cortex_T8 | Cortex | T8 | AT2G31570 | GPX2 | 0.585 | 24 | 10 | 22 | 3 | 0.9757576 | 0.9757576 |
| 0.859 | 2.324442 | 0.718 | 0.873 | 0.344 | Cortex_T8 | Cortex | T8 | AT4G37010 | CEN2 | 0.529 | 56 | 19 | 27 | 10 | 0.9636364 | 0.9636364 |
| 0.933 | 2.219710 | 0.866 | 0.976 | 0.181 | Cortex_T8 | Cortex | T8 | AT5G15180 | PER56 | 0.795 | 1 | 36 | 1 | 1 | 0.9515152 | 0.9515152 |
| 0.838 | 2.193481 | 0.676 | 0.834 | 0.170 | Cortex_T8 | Cortex | T8 | AT5G44130 | FLA13 | 0.664 | 8 | 43 | 38 | 9 | 0.9515152 | 0.9515152 |
| 0.895 | 1.943125 | 0.790 | 0.965 | 0.311 | Cortex_T8 | Cortex | T8 | AT5G53370 | ATPMEPCRF | 0.654 | 10 | 93 | 7 | 12 | 0.9515152 | 0.9515152 |
| 0.875 | 1.967181 | 0.750 | 0.820 | 0.180 | Cortex_T8 | Cortex | T8 | AT5G63600 | FLS5 | 0.640 | 13 | 87 | 15 | 16 | 0.9515152 | 0.9515152 |
| 0.835 | 2.402254 | 0.670 | 0.797 | 0.274 | Cortex_T8 | Cortex | T8 | AT3G28940 | AIG2B | 0.523 | 61 | 11 | 44 | 18 | 0.9515152 | 0.9515152 |
| 0.792 | 2.103887 | 0.584 | 0.719 | 0.199 | Cortex_T8 | Cortex | T8 | AT4G09760 | AT4G09760 | 0.520 | 63 | 61 | 95 | 45 | 0.6484848 | 0.6484848 |
| 0.885 | 3.748602 | 0.770 | 0.928 | 0.335 | Cortex_T9 | Cortex | T9 | AT3G48890 | MSBP2 | 0.593 | 49 | 1 | 26 | 7 | 0.9878788 | 0.9878788 |
| 0.920 | 2.949297 | 0.840 | 0.948 | 0.237 | Cortex_T9 | Cortex | T9 | AT5G19230 | AT5G19230 | 0.711 | 8 | 28 | 11 | 4 | 0.9757576 | 0.9757576 |
| 0.878 | 2.891494 | 0.756 | 0.873 | 0.199 | Cortex_T9 | Cortex | T9 | AT3G18170 | AT3G18170 | 0.674 | 19 | 32 | 33 | 11 | 0.9757576 | 0.9757576 |
| 0.888 | 2.832023 | 0.776 | 0.796 | 0.189 | Cortex_T9 | Cortex | T9 | AT4G25900 | AT4G25900 | 0.607 | 40 | 34 | 24 | 14 | 0.9757576 | 0.9757576 |
| 0.929 | 2.659444 | 0.858 | 0.958 | 0.203 | Cortex_T9 | Cortex | T9 | AT5G44380 | AT5G44380 | 0.755 | 5 | 61 | 6 | 6 | 0.9515152 | 0.9515152 |
| 0.872 | 2.820674 | 0.744 | 0.865 | 0.146 | Cortex_T9 | Cortex | T9 | AT2G27920 | SCPL51 | 0.719 | 7 | 35 | 35 | 9 | 0.9515152 | 0.9515152 |
| 0.880 | 3.077648 | 0.760 | 0.865 | 0.239 | Cortex_T9 | Cortex | T9 | AT4G15610 | AT4G15610 | 0.626 | 31 | 19 | 30 | 10 | 0.9515152 | 0.9515152 |
| 0.871 | 3.186065 | 0.742 | 0.921 | 0.347 | Cortex_T9 | Cortex | T9 | AT3G17420 | GPK1 | 0.574 | 56 | 10 | 36 | 15 | 0.9515152 | 0.9515152 |
| 0.894 | 2.733063 | 0.788 | 0.967 | 0.420 | Cortex_T9 | Cortex | T9 | AT1G08930 | ERD6 | 0.547 | 75 | 43 | 20 | 20 | 0.9515152 | 0.9515152 |
| myAUC | avg_diff | power | pct.1 | pct.2 | cluster | celltype | stage | gene | Name | pct.diff | pct.diff_rank | avg_diff_rank | myAUC_rank | combined_rank | long_cor | abs_long_cor |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <fct> | <chr> | <fct> | <chr> | <chr> | <dbl> | <int> | <int> | <int> | <int> | <dbl> | <dbl> |
| 0.962 | 2.841572 | 0.924 | 0.988 | 0.117 | Cortex_T0 | Cortex | T0 | AT5G28060 | RPS24B | 0.871 | 115 | 178 | 47 | 9 | -0.8787879 | 0.8787879 |
| 0.967 | 2.712818 | 0.934 | 1.000 | 0.136 | Cortex_T0 | Cortex | T0 | AT2G27720 | AT2G27720 | 0.864 | 135 | 269 | 5 | 13 | -0.8787879 | 0.8787879 |
| 0.964 | 2.682942 | 0.928 | 0.998 | 0.124 | Cortex_T0 | Cortex | T0 | AT3G02080 | RPS19A | 0.874 | 102 | 302 | 19 | 14 | -0.8303030 | 0.8303030 |
| 0.965 | 2.616760 | 0.930 | 0.997 | 0.106 | Cortex_T0 | Cortex | T0 | AT5G16130 | RPS7C | 0.891 | 39 | 345 | 14 | 12 | -0.7939394 | 0.7939394 |
| 0.970 | 2.844078 | 0.940 | 1.000 | 0.096 | Cortex_T0 | Cortex | T0 | AT1G27400 | RPL17A | 0.904 | 12 | 175 | 1 | 4 | -0.7818182 | 0.7818182 |
| 0.966 | 2.603655 | 0.932 | 1.000 | 0.096 | Cortex_T0 | Cortex | T0 | AT5G45775 | RPL11C | 0.904 | 13 | 353 | 9 | 11 | -0.7818182 | 0.7818182 |
| 0.967 | 2.697931 | 0.934 | 1.000 | 0.102 | Cortex_T0 | Cortex | T0 | AT3G16080 | RPL37C | 0.898 | 25 | 284 | 6 | 7 | -0.7090909 | 0.7090909 |
| 0.967 | 2.694637 | 0.934 | 0.998 | 0.093 | Cortex_T0 | Cortex | T0 | AT3G45030 | RPS20C | 0.905 | 11 | 287 | 7 | 6 | -0.6242424 | 0.6242424 |
| 0.965 | 2.575404 | 0.930 | 0.990 | 0.105 | Cortex_T0 | Cortex | T0 | AT3G62530 | AT3G62530 | 0.885 | 65 | 391 | 15 | 17 | -0.5878788 | 0.5878788 |
| 0.956 | 2.843506 | 0.912 | 0.971 | 0.114 | Cortex_T0 | Cortex | T0 | AT3G13580 | RPL7D | 0.857 | 158 | 176 | 147 | 20 | -0.5636364 | 0.5636364 |
| 0.949 | 2.995861 | 0.898 | 0.970 | 0.119 | Cortex_T1 | Cortex | T1 | AT2G01250 | RPL7B | 0.851 | 42 | 129 | 15 | 5 | -0.9272727 | 0.9272727 |
| 0.948 | 3.017097 | 0.896 | 0.964 | 0.117 | Cortex_T1 | Cortex | T1 | AT5G23740 | RPS11C | 0.847 | 54 | 117 | 24 | 6 | -0.9272727 | 0.9272727 |
| 0.950 | 2.797067 | 0.900 | 0.988 | 0.120 | Cortex_T1 | Cortex | T1 | AT5G15200 | RPS9B | 0.868 | 15 | 240 | 6 | 17 | -0.9272727 | 0.9272727 |
| 0.947 | 2.813544 | 0.894 | 0.985 | 0.119 | Cortex_T1 | Cortex | T1 | AT4G27090 | RPL14B | 0.866 | 18 | 227 | 38 | 18 | -0.9151515 | 0.9151515 |
| 0.949 | 2.975505 | 0.898 | 0.964 | 0.127 | Cortex_T1 | Cortex | T1 | AT1G56045 | RPL41G | 0.837 | 74 | 139 | 16 | 10 | -0.8909091 | 0.8909091 |
| 0.951 | 2.812709 | 0.902 | 0.988 | 0.109 | Cortex_T1 | Cortex | T1 | AT5G27850 | RPL18C | 0.879 | 4 | 228 | 2 | 12 | -0.8909091 | 0.8909091 |
| 0.947 | 2.950026 | 0.894 | 0.979 | 0.128 | Cortex_T1 | Cortex | T1 | AT3G02560 | RPS7B | 0.851 | 44 | 157 | 36 | 13 | -0.8909091 | 0.8909091 |
| 0.951 | 2.775165 | 0.902 | 0.988 | 0.125 | Cortex_T1 | Cortex | T1 | AT3G25520 | ATL5 | 0.863 | 21 | 264 | 3 | 20 | -0.8909091 | 0.8909091 |
| 0.947 | 2.970321 | 0.894 | 0.970 | 0.118 | Cortex_T1 | Cortex | T1 | AT1G22780 | RPS18C | 0.852 | 38 | 143 | 35 | 8 | -0.8787879 | 0.8787879 |
| 0.949 | 2.926049 | 0.898 | 0.976 | 0.125 | Cortex_T1 | Cortex | T1 | AT5G58420 | RPS4D | 0.851 | 47 | 164 | 17 | 9 | -0.8787879 | 0.8787879 |
| 0.857 | 2.403694 | 0.714 | 0.830 | 0.247 | Cortex_T2 | Cortex | T2 | AT1G17285 | AT1G17285 | 0.583 | 7 | 24 | 3 | 4 | -0.9878788 | 0.9878788 |
| 0.881 | 2.655178 | 0.762 | 0.878 | 0.227 | Cortex_T2 | Cortex | T2 | AT5G14020 | AT5G14020 | 0.651 | 1 | 9 | 1 | 1 | -0.9757576 | 0.9757576 |
| 0.809 | 2.229940 | 0.618 | 0.793 | 0.256 | Cortex_T2 | Cortex | T2 | AT2G24280 | AT2G24280 | 0.537 | 20 | 41 | 34 | 13 | -0.9757576 | 0.9757576 |
| 0.840 | 2.225051 | 0.680 | 0.710 | 0.165 | Cortex_T2 | Cortex | T2 | AT1G54000 | GLL22 | 0.545 | 18 | 42 | 10 | 9 | -0.9636364 | 0.9636364 |
| 0.831 | 1.791538 | 0.662 | 0.815 | 0.224 | Cortex_T2 | Cortex | T2 | AT1G32190 | AT1G32190 | 0.591 | 5 | 95 | 15 | 16 | -0.9393939 | 0.9393939 |
| 0.844 | 2.812988 | 0.688 | 0.886 | 0.406 | Cortex_T2 | Cortex | T2 | AT3G19820 | DIM | 0.480 | 66 | 5 | 6 | 11 | -0.9151515 | 0.9151515 |
| 0.843 | 1.745310 | 0.686 | 0.862 | 0.230 | Cortex_T2 | Cortex | T2 | AT1G26945 | PRE6 | 0.632 | 2 | 105 | 7 | 15 | -0.9151515 | 0.9151515 |
| 0.788 | 2.641667 | 0.576 | 0.710 | 0.211 | Cortex_T2 | Cortex | T2 | AT1G62810 | AT1G62810 | 0.499 | 43 | 10 | 72 | 18 | -0.9030303 | 0.9030303 |
| 0.847 | 2.965077 | 0.694 | 0.700 | 0.165 | Cortex_T2 | Cortex | T2 | AT2G45050 | GATA2 | 0.535 | 21 | 1 | 5 | 2 | -0.8666667 | 0.8666667 |
| 0.827 | 2.357117 | 0.654 | 0.688 | 0.164 | Cortex_T2 | Cortex | T2 | AT2G20515 | AT2G20515 | 0.524 | 29 | 27 | 17 | 10 | -0.8666667 | 0.8666667 |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| 0.867 | 1.663836 | 0.734 | 0.954 | 0.345 | Cortex_T6 | Cortex | T6 | AT2G39010 | PIP2-6 | 0.609 | 2 | 10 | 1 | 1 | 0.5878788 | 0.5878788 |
| 0.823 | 1.463082 | 0.646 | 0.914 | 0.343 | Cortex_T6 | Cortex | T6 | AT5G64620 | C/VIF2 | 0.571 | 6 | 26 | 11 | 2 | 0.5151515 | 0.5151515 |
| 0.808 | 1.655623 | 0.616 | 0.905 | 0.403 | Cortex_T6 | Cortex | T6 | AT5G66920 | sks17 | 0.502 | 19 | 13 | 16 | 4 | 0.5151515 | 0.5151515 |
| 0.823 | 1.463082 | 0.646 | 0.914 | 0.343 | Cortex_T6 | Cortex | T6 | AT5G64620 | C/VIF2 | 0.571 | 6 | 26 | 11 | 2 | 0.5151515 | 0.5151515 |
| 0.703 | 1.040975 | 0.406 | 0.734 | 0.282 | Cortex_T6 | Cortex | T6 | AT3G21670 | NPF6.4 | 0.452 | 51 | 96 | 198 | 121 | 0.4909091 | 0.4909091 |
| 0.816 | 1.464443 | 0.632 | 0.842 | 0.272 | Cortex_T7 | Cortex | T7 | AT4G25830 | AT4G25830 | 0.570 | 6 | 44 | 17 | 6 | 0.9515152 | 0.9515152 |
| 0.848 | 1.151143 | 0.696 | 0.977 | 0.382 | Cortex_T7 | Cortex | T7 | AT3G57020 | SSL9 | 0.595 | 4 | 80 | 4 | 11 | 0.9515152 | 0.9515152 |
| 0.835 | 1.257908 | 0.670 | 0.915 | 0.393 | Cortex_T7 | Cortex | T7 | AT4G23400 | PIP1-5 | 0.522 | 18 | 70 | 8 | 12 | 0.9515152 | 0.9515152 |
| 0.790 | 1.334410 | 0.580 | 0.793 | 0.276 | Cortex_T7 | Cortex | T7 | AT4G02700 | SULTR3;2 | 0.517 | 19 | 58 | 34 | 20 | 0.9393939 | 0.9393939 |
| 0.816 | 1.726037 | 0.632 | 0.746 | 0.202 | Cortex_T7 | Cortex | T7 | AT4G00330 | CRCK2 | 0.544 | 13 | 21 | 16 | 3 | 0.9272727 | 0.9272727 |
| 0.829 | 1.136766 | 0.658 | 0.937 | 0.376 | Cortex_T7 | Cortex | T7 | AT3G14690 | CYP72A15 | 0.561 | 7 | 82 | 11 | 15 | 0.9272727 | 0.9272727 |
| 0.804 | 1.752173 | 0.608 | 0.720 | 0.175 | Cortex_T7 | Cortex | T7 | AT5G25810 | TINY | 0.545 | 12 | 18 | 27 | 5 | 0.9151515 | 0.9151515 |
| 0.793 | 1.969611 | 0.586 | 0.666 | 0.202 | Cortex_T7 | Cortex | T7 | AT1G66725 | MIR163 | 0.464 | 37 | 10 | 33 | 10 | 0.9151515 | 0.9151515 |
| 0.863 | 2.411867 | 0.726 | 0.777 | 0.192 | Cortex_T8 | Cortex | T8 | AT2G31570 | GPX2 | 0.585 | 24 | 10 | 22 | 3 | 0.9757576 | 0.9757576 |
| 0.859 | 2.324442 | 0.718 | 0.873 | 0.344 | Cortex_T8 | Cortex | T8 | AT4G37010 | CEN2 | 0.529 | 56 | 19 | 27 | 10 | 0.9636364 | 0.9636364 |
| 0.933 | 2.219710 | 0.866 | 0.976 | 0.181 | Cortex_T8 | Cortex | T8 | AT5G15180 | PER56 | 0.795 | 1 | 36 | 1 | 1 | 0.9515152 | 0.9515152 |
| 0.838 | 2.193481 | 0.676 | 0.834 | 0.170 | Cortex_T8 | Cortex | T8 | AT5G44130 | FLA13 | 0.664 | 8 | 43 | 38 | 9 | 0.9515152 | 0.9515152 |
| 0.895 | 1.943125 | 0.790 | 0.965 | 0.311 | Cortex_T8 | Cortex | T8 | AT5G53370 | ATPMEPCRF | 0.654 | 10 | 93 | 7 | 12 | 0.9515152 | 0.9515152 |
| 0.875 | 1.967181 | 0.750 | 0.820 | 0.180 | Cortex_T8 | Cortex | T8 | AT5G63600 | FLS5 | 0.640 | 13 | 87 | 15 | 16 | 0.9515152 | 0.9515152 |
| 0.835 | 2.402254 | 0.670 | 0.797 | 0.274 | Cortex_T8 | Cortex | T8 | AT3G28940 | AIG2B | 0.523 | 61 | 11 | 44 | 18 | 0.9515152 | 0.9515152 |
| 0.792 | 2.103887 | 0.584 | 0.719 | 0.199 | Cortex_T8 | Cortex | T8 | AT4G09760 | AT4G09760 | 0.520 | 63 | 61 | 95 | 45 | 0.6484848 | 0.6484848 |
| 0.885 | 3.748602 | 0.770 | 0.928 | 0.335 | Cortex_T9 | Cortex | T9 | AT3G48890 | MSBP2 | 0.593 | 49 | 1 | 26 | 7 | 0.9878788 | 0.9878788 |
| 0.920 | 2.949297 | 0.840 | 0.948 | 0.237 | Cortex_T9 | Cortex | T9 | AT5G19230 | AT5G19230 | 0.711 | 8 | 28 | 11 | 4 | 0.9757576 | 0.9757576 |
| 0.878 | 2.891494 | 0.756 | 0.873 | 0.199 | Cortex_T9 | Cortex | T9 | AT3G18170 | AT3G18170 | 0.674 | 19 | 32 | 33 | 11 | 0.9757576 | 0.9757576 |
| 0.888 | 2.832023 | 0.776 | 0.796 | 0.189 | Cortex_T9 | Cortex | T9 | AT4G25900 | AT4G25900 | 0.607 | 40 | 34 | 24 | 14 | 0.9757576 | 0.9757576 |
| 0.929 | 2.659444 | 0.858 | 0.958 | 0.203 | Cortex_T9 | Cortex | T9 | AT5G44380 | AT5G44380 | 0.755 | 5 | 61 | 6 | 6 | 0.9515152 | 0.9515152 |
| 0.872 | 2.820674 | 0.744 | 0.865 | 0.146 | Cortex_T9 | Cortex | T9 | AT2G27920 | SCPL51 | 0.719 | 7 | 35 | 35 | 9 | 0.9515152 | 0.9515152 |
| 0.880 | 3.077648 | 0.760 | 0.865 | 0.239 | Cortex_T9 | Cortex | T9 | AT4G15610 | AT4G15610 | 0.626 | 31 | 19 | 30 | 10 | 0.9515152 | 0.9515152 |
| 0.871 | 3.186065 | 0.742 | 0.921 | 0.347 | Cortex_T9 | Cortex | T9 | AT3G17420 | GPK1 | 0.574 | 56 | 10 | 36 | 15 | 0.9515152 | 0.9515152 |
| 0.894 | 2.733063 | 0.788 | 0.967 | 0.420 | Cortex_T9 | Cortex | T9 | AT1G08930 | ERD6 | 0.547 | 75 | 43 | 20 | 20 | 0.9515152 | 0.9515152 |
write.csv(genes_to_plt_endo, "./supp_data/consensus_time_endo_to_plot.csv", row.names=F)
write.csv(genes_to_plt_cortex, "./supp_data/consensus_time_cortex_to_plot.csv", row.names=F)
# subset for endodermis
Endo_QC <- subset(rc.integrated, celltype.anno %in% c("Quiescent Center", "Endodermis"))
# pseudobulk of each stage of endodermis
afm <- as.matrix(Endo_QC@assays$integrated@data)
pooled_endo <- matrix(nrow=nrow(afm), ncol = 0)
for (i in unique(Endo_QC@meta.data$consensus.time.group)) {
m <- afm[,which(Endo_QC@meta.data$consensus.time.group==i)]
pooled_endo <- cbind(pooled_endo, rowSums(m)/ncol(m))
}
colnames(pooled_endo) <- unique(Endo_QC@meta.data$consensus.time.group)
(endo_sub_m <- pooled_endo[genes_to_plt_endo, c("T0", "T1", "T2", "T3", "T4", "T5", "T6", "T7", "T8", "T9")])
| T0 | T1 | T2 | T3 | T4 | T5 | T6 | T7 | T8 | T9 | |
|---|---|---|---|---|---|---|---|---|---|---|
| AT2G15300 | -0.14242723 | -0.16149722 | -2.809425e-01 | -0.33057376 | -0.31115196 | -0.27073994 | 0.09957142 | 0.42311098 | 1.9529662 | 6.69348303 |
| AT1G71740 | -0.35660894 | -0.38861004 | -4.704698e-01 | -0.45982226 | -0.44527083 | -0.44129964 | -0.28372146 | 1.69033522 | 5.1668984 | 8.56355676 |
| AT3G11550 | -0.45387346 | -0.47447793 | -5.831723e-01 | -0.57034652 | -0.53650431 | -0.49510965 | -0.02590912 | 3.19715514 | 6.8916465 | 9.19329727 |
| AT2G39430 | -0.44548211 | -0.40422254 | -5.372530e-01 | -0.51568935 | -0.50679208 | -0.49683335 | -0.20074373 | 1.85296777 | 5.2198797 | 9.55926738 |
| AT5G06200 | -0.32523428 | -0.41466255 | -5.043669e-01 | -0.46422293 | -0.47391101 | -0.43037394 | -0.28721650 | 1.00965944 | 4.5592723 | 9.10937747 |
| AT5G65020 | -1.00819942 | -0.69093475 | -3.756301e-01 | -0.30468028 | -0.34045204 | -0.14226229 | 0.31271816 | 1.29149919 | 2.0227179 | 3.89940521 |
| AT2G28671 | -0.35460516 | -0.36516862 | -3.968545e-01 | -0.38767272 | -0.32261326 | 0.03630028 | 0.85361903 | 3.40586000 | 5.8363485 | 8.06132472 |
| AT1G44970 | -0.28789572 | -0.28097155 | -3.083765e-01 | -0.18732854 | -0.15816977 | -0.08031299 | 0.11728710 | 1.19911422 | 3.4993281 | 8.67665303 |
| AT5G44790 | -0.76083064 | -0.81538100 | -7.564502e-01 | -0.69014925 | -0.63201968 | -0.47639592 | -0.24766409 | 0.08388293 | 0.7781348 | 4.31773659 |
| AT4G34050 | -1.78984712 | -1.90736562 | -6.352310e-01 | -0.14155373 | 0.25091423 | 0.90158277 | 1.93458694 | 1.12839587 | 0.9368397 | 8.30696836 |
| AT2G27370 | -0.50029044 | -0.50486636 | -1.774493e-01 | -0.04975765 | 0.20792688 | 0.52270686 | 0.86990819 | 1.21404431 | 3.1665410 | 9.37294065 |
| AT2G36100 | -0.51355613 | -0.73281177 | -9.928055e-01 | -0.95666284 | -0.91629516 | -0.56717615 | 2.45439191 | 7.79884294 | 9.6092401 | 9.95081880 |
| AT5G08240 | -0.27700742 | -0.34189126 | -2.553061e-01 | -0.30848236 | -0.12210478 | 0.18298834 | 0.99379532 | 2.60528658 | 3.2669372 | 0.30265366 |
| AT3G14280 | -0.72448509 | -0.94559051 | -9.690169e-01 | -0.98463245 | -0.88933492 | -0.72934232 | -0.01771861 | 2.56127653 | 3.4632678 | 0.96909351 |
| AT3G05937 | -0.36738608 | -0.46762040 | -4.958722e-01 | -0.47195996 | -0.46186238 | -0.45072244 | -0.11008450 | 1.34889622 | 1.6747880 | -0.10704136 |
| AT4G13580 | -0.48109373 | -0.59546225 | -5.659305e-01 | -0.53690441 | -0.50600947 | -0.44874098 | 0.18975921 | 4.57491933 | 7.7580452 | 8.91861860 |
| AT1G03850 | -1.16423041 | -1.25070429 | -1.348715e+00 | -1.44590686 | -1.45407896 | -1.40485683 | -0.55767638 | 3.27082006 | 4.6186920 | -0.32723453 |
| AT3G03520 | -0.59844104 | -0.68936662 | -5.969454e-01 | -0.58591014 | -0.49933465 | -0.19306077 | 0.55340479 | 1.40525730 | 2.1205917 | 2.87664476 |
| AT4G37790 | -0.66752120 | -0.79582544 | -6.866044e-01 | -0.71057285 | -0.24879277 | 0.82081914 | 2.38442758 | 3.14958774 | 3.4099629 | 0.03788676 |
| AT4G21620 | -0.05369942 | -0.07590941 | -7.095406e-02 | -0.07692939 | -0.07828367 | -0.05389582 | 0.02134841 | 0.53912513 | 0.6530873 | 0.14042561 |
| AT4G34230 | -1.06191982 | -1.39337138 | -1.308467e+00 | -1.11219673 | -0.49651345 | 1.24639547 | 2.99859374 | 2.96681343 | 2.4773615 | 0.87865701 |
| AT1G35260 | -0.49361851 | -0.56419115 | 5.535556e-01 | 2.02711131 | 2.67586303 | 3.13618595 | 3.33295066 | 4.34727150 | 4.9797674 | 2.18027557 |
| AT2G15340 | -0.24379921 | -0.19570308 | 7.277600e-02 | 0.16201485 | 0.55413515 | 1.44069699 | 2.99404419 | 4.10444530 | 3.5684940 | 0.31115815 |
| AT4G23493 | -0.16169833 | -0.05200886 | 1.979299e-01 | 0.25499557 | 0.32146983 | 0.50622072 | 0.81983407 | 1.32412540 | 1.5062300 | 0.83188347 |
| AT5G66390 | -0.75829852 | -0.83186349 | -7.653330e-01 | -0.73368548 | -0.43265705 | 0.98855808 | 4.51154625 | 7.99520385 | 9.2026198 | 9.79796924 |
| AT3G09270 | -0.97914137 | -0.92688327 | -5.706325e-01 | 0.09600136 | 0.89512897 | 1.68951062 | 2.36409743 | 3.53342921 | 3.8430070 | 2.42631678 |
| AT3G06125 | -0.60443069 | -0.43269097 | 8.743106e-05 | 0.49842413 | 0.85137943 | 1.23874191 | 2.33089604 | 4.74458252 | 5.7413495 | 4.26022675 |
| AT4G15960 | -0.58179070 | -0.68583456 | -3.155279e-01 | 0.14496414 | 0.72251809 | 1.45006409 | 1.73112141 | 0.91634507 | 0.6757686 | 0.38246189 |
| AT3G13520 | -1.37220147 | -1.03789693 | 1.532634e+00 | 2.16087968 | 2.90593199 | 3.91355324 | 4.44137629 | 4.32409005 | 4.1391877 | 0.75889705 |
| AT3G48350 | -0.26788403 | -0.23252882 | -6.986186e-02 | 0.03060283 | 0.57255740 | 1.47843302 | 2.05287986 | 0.63768838 | 0.1729415 | -0.08603755 |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| AT5G55730 | 0.7301355 | 0.8090575 | 2.5678981 | 2.0777407 | 1.2113615 | 0.18219065 | -0.42325776 | -0.62789472 | -0.7088659 | -0.6319220 |
| AT5G07030 | 2.8050195 | 1.5060868 | 2.1289931 | 0.4334027 | -0.4513561 | -0.88581173 | -1.01038801 | -0.93587124 | -0.9431494 | -0.8522577 |
| AT4G39900 | 0.4004057 | 1.3886226 | 2.4839831 | 1.8592118 | 0.9826779 | 0.36228791 | 0.05387223 | -0.14073418 | -0.2418469 | -0.3653124 |
| AT2G43360 | 1.2852430 | 2.3943542 | 2.0400653 | 0.9542262 | 0.3744483 | -0.04831887 | -0.23456547 | -0.32029943 | -0.3186371 | -0.1348833 |
| AT1G54580 | 2.4487875 | 4.0945902 | 5.5231830 | 3.5103594 | 1.5934715 | 0.13717758 | -0.42405624 | -0.73240974 | -0.9145339 | -0.8148472 |
| AT2G30200 | 1.7032993 | 2.2281979 | 2.6501361 | 1.5612248 | 0.7421746 | 0.05982531 | -0.34158985 | -0.48462647 | -0.5185469 | -0.4150099 |
| AT2G05990 | 2.3496195 | 3.3683938 | 3.8579667 | 2.3118050 | 1.1542319 | 0.23505782 | -0.10356638 | -0.44658022 | -0.6600482 | -0.4646967 |
| AT4G16265 | 1.1230050 | 1.6492551 | 2.4688246 | 1.8431108 | 1.4007037 | 0.97757805 | 0.53250412 | 0.01904131 | -0.2006307 | -0.2027613 |
| AT3G23390 | 6.2142828 | 4.5596509 | -0.4297028 | -1.0822531 | -1.4014637 | -1.58358349 | -1.60722642 | -1.47562475 | -1.4656884 | -1.2936825 |
| AT2G44120 | 5.3386589 | 3.9173700 | -0.5394960 | -0.9866326 | -1.1646553 | -1.28440055 | -1.31444509 | -1.22345072 | -1.1814329 | -1.0534027 |
| AT1G09590 | 5.8605227 | 4.4474440 | -0.3573291 | -0.9283873 | -1.1598000 | -1.29736320 | -1.29019645 | -1.10303056 | -1.0810291 | -0.9349805 |
| AT3G55750 | 6.0717685 | 4.4427731 | -0.3726595 | -0.9141344 | -1.1537023 | -1.27974321 | -1.31503654 | -1.13260243 | -1.1334568 | -1.0689091 |
| AT4G17390 | 5.4276392 | 3.8748100 | -0.3934553 | -0.9273360 | -1.1425201 | -1.29053841 | -1.31350804 | -1.21653273 | -1.2237207 | -1.1653592 |
| AT1G72370 | 6.2600967 | 4.5042008 | -0.4146206 | -1.0762066 | -1.3686621 | -1.54143467 | -1.53334547 | -1.41357058 | -1.3910397 | -1.3553782 |
| AT3G09200 | 6.2909812 | 4.4450343 | -0.2888330 | -0.8700513 | -1.1717659 | -1.31294716 | -1.36872318 | -1.22467377 | -1.2697066 | -1.2465645 |
| AT5G15200 | 5.3735738 | 4.0782352 | -0.5067444 | -1.0256581 | -1.2427727 | -1.35934329 | -1.40214375 | -1.31463833 | -1.3516948 | -1.2932665 |
| AT5G23740 | 5.8488341 | 4.4577998 | -0.5121212 | -1.0166777 | -1.2135075 | -1.35567896 | -1.40429675 | -1.36583655 | -1.3702588 | -1.2953544 |
| AT3G62250 | 5.2396468 | 4.0852979 | -0.1247129 | -0.7419270 | -1.0405571 | -1.19937011 | -1.19944894 | -1.01356115 | -1.0188779 | -1.0842226 |
| AT5G16130 | 8.7414625 | 5.3445527 | -0.5962779 | -1.3774850 | -1.7005758 | -1.89748813 | -1.92982673 | -1.77826124 | -1.7345597 | -1.6766437 |
| AT4G16720 | 7.5221448 | 4.9888458 | -0.8093254 | -1.4384086 | -1.7087000 | -1.85370291 | -1.84689724 | -1.68557445 | -1.6392852 | -1.6203207 |
| AT4G15000 | 6.8672763 | 4.6417626 | -0.4740812 | -1.2327746 | -1.5330334 | -1.67733837 | -1.67124782 | -1.47479762 | -1.3968493 | -1.2754481 |
| AT3G11510 | 7.2585245 | 5.0546565 | -0.5311614 | -1.3338677 | -1.6654568 | -1.85770725 | -1.88197263 | -1.74540058 | -1.7073625 | -1.6488258 |
| AT2G27530 | 4.1757220 | 2.9452826 | -0.6267409 | -1.0264489 | -1.1620509 | -1.18784162 | -1.15379127 | -1.01715070 | -1.0508467 | -1.1665010 |
| AT1G70600 | 5.7410246 | 4.2510042 | -0.3639923 | -1.1240070 | -1.4462404 | -1.62412733 | -1.64096479 | -1.46608023 | -1.4374359 | -1.4353937 |
| AT5G02450 | 4.9093378 | 3.3948316 | -0.2406399 | -0.7834026 | -1.0925696 | -1.23727379 | -1.23249726 | -1.11710542 | -1.0882024 | -1.0854760 |
| AT5G02960 | 8.1821150 | 5.4831365 | -0.4194876 | -1.3335844 | -1.7448029 | -1.97707080 | -2.01581882 | -1.86506820 | -1.8779279 | -1.8504664 |
| AT5G27850 | 6.3158525 | 4.3083371 | -0.7171787 | -1.2037148 | -1.4211263 | -1.55899730 | -1.59421486 | -1.51407829 | -1.5174841 | -1.4320561 |
| AT3G56340 | 5.8095825 | 4.0063386 | -0.5257235 | -1.2267011 | -1.5099342 | -1.64956692 | -1.68118999 | -1.59981529 | -1.5516093 | -1.5311076 |
| AT4G31700 | 4.7459831 | 3.4037189 | -0.1995999 | -0.8129013 | -1.0987796 | -1.25886305 | -1.25695927 | -1.14372572 | -1.1487195 | -1.1171770 |
| AT3G60245 | 7.0449274 | 4.9107791 | -0.4235197 | -1.1278805 | -1.4158444 | -1.59340172 | -1.58224810 | -1.40767588 | -1.4079721 | -1.4325733 |
# quantile normalize
mat = endo_sub_m
mat2 = t(apply(mat, 1, function(x) {
q10 = quantile(x, 0.1)
q90 = quantile(x, 0.9)
x[x < q10] = q10
x[x > q90] = q90
scale(x)
}))
colnames(mat2) = colnames(mat)
# side annotation with color to match umap
endo_sa = rowAnnotation(foo = anno_block(gp = gpar(fill = "#0000FF"),
labels = c("Endodermis"),
labels_gp = gpar(col = "white", fontsize = 18)))
# genes to mark on side of heatmap
(endo_mat_for_mark <- data.frame(mat2) %>%
rownames_to_column("gene") %>%
left_join(feature_names) %>%
mutate(index=dplyr::row_number()) %>%
select(Name, index) %>%
filter(Name %in% c("XTH16", "SCR", "MYB36", "CASP1", "CASP2", "CASP3")))
Joining, by = "gene"
| Name | index |
|---|---|
| <chr> | <int> |
| CASP2 | 3 |
| CASP3 | 11 |
| CASP1 | 12 |
| MYB36 | 36 |
| SCR | 61 |
| XTH16 | 63 |
# at - index of genes you want to mark
# labels - Names to show
endo_mark_anno = rowAnnotation(foo = anno_mark(at = endo_mat_for_mark$index, labels = endo_mat_for_mark$Name, labels_gp = gpar(col = "black", fontsize = 16)))
options(repr.plot.width=10, repr.plot.height=8)
Endo_hm <- Heatmap(mat2,
col = colorRamp2(c(-1.5, 0, 1.5),
c('blue','white','red')),
show_column_names = T,
cluster_columns = F,
cluster_rows=F,
show_row_names = F,
left_annotation=endo_sa,
right_annotation=endo_mark_anno,
heatmap_legend_param = list(title_position="topcenter", title = "Expression", direction="horizontal"))
draw(Endo_hm, padding = unit(c(10, 10, 10, 10), "mm"), heatmap_legend_side = "top")
# cortex subset
Cor_QC <- subset(rc.integrated, celltype.anno %in% c("Quiescent Center", "Cortex"))
# pseudobulk of each stage of cortex
afm <- as.matrix(Cor_QC@assays$integrated@data)
pooled_cortex <- matrix(nrow=nrow(afm), ncol = 0)
for (i in unique(Cor_QC@meta.data$consensus.time.group)) {
m <- afm[,which(Cor_QC@meta.data$consensus.time.group==i)]
pooled_cortex <- cbind(pooled_cortex, rowSums(m)/ncol(m))
}
colnames(pooled_cortex) <- unique(Cor_QC@meta.data$consensus.time.group)
(cor_sub_m <- pooled_cortex[genes_to_plt_cortex, c("T0", "T1", "T2", "T3", "T4", "T5", "T6", "T7", "T8", "T9")])
| T0 | T1 | T2 | T3 | T4 | T5 | T6 | T7 | T8 | T9 | |
|---|---|---|---|---|---|---|---|---|---|---|
| AT5G28060 | 3.3618492 | 2.6299378 | -0.073066518 | -0.8474143 | -0.98969054 | -1.1703605 | -1.268575179 | -1.31155911 | -1.37317022 | -1.40318396 |
| AT2G27720 | 3.8613899 | 3.0233971 | 0.134892414 | -0.5785870 | -0.74875052 | -0.8763586 | -1.070331353 | -1.12689923 | -1.16017116 | -1.20657080 |
| AT3G02080 | 3.4246586 | 2.7404931 | -0.059228205 | -0.7242290 | -0.82861098 | -0.9228851 | -1.013056434 | -1.03356621 | -1.04725742 | -1.10604766 |
| AT5G16130 | 7.8747834 | 5.6665560 | -0.104457378 | -1.3917178 | -1.58696732 | -1.7622831 | -1.893205932 | -1.86407705 | -1.87133041 | -1.90693716 |
| AT1G27400 | 8.6212721 | 5.7445302 | -0.393651039 | -1.6408461 | -1.82125725 | -1.9811820 | -2.067151010 | -2.07150361 | -2.10114890 | -2.11542489 |
| AT5G45775 | 7.5149917 | 5.1948935 | -0.131228698 | -1.3315355 | -1.54532984 | -1.6877456 | -1.770982082 | -1.75838575 | -1.77343643 | -1.80507639 |
| AT3G16080 | 8.1424800 | 5.6297957 | 0.097099207 | -1.4047155 | -1.67514368 | -1.8402602 | -1.932430762 | -1.89338502 | -1.93443066 | -1.95262379 |
| AT3G45030 | 7.8812068 | 5.2848012 | -0.604960919 | -1.5217063 | -1.62330267 | -1.6821780 | -1.734441332 | -1.72134059 | -1.74396387 | -1.79158357 |
| AT3G62530 | 6.6559972 | 5.0625430 | -0.018679339 | -0.9486519 | -1.04881295 | -1.1142400 | -1.170516840 | -1.14192258 | -1.07853332 | -1.06305724 |
| AT3G13580 | 3.1904841 | 2.3151531 | -0.244782986 | -0.5234968 | -0.58842122 | -0.6335214 | -0.690727363 | -0.62127948 | -0.64374928 | -0.68322709 |
| AT2G01250 | 5.9062186 | 4.8376718 | -0.042753974 | -1.0671940 | -1.26087097 | -1.4006699 | -1.520077185 | -1.55486651 | -1.56722159 | -1.60753480 |
| AT5G23740 | 5.2427375 | 4.4274909 | -0.187092773 | -1.0925899 | -1.27987082 | -1.4002439 | -1.484831185 | -1.50604150 | -1.54163399 | -1.57561474 |
| AT5G15200 | 4.7821580 | 4.0877754 | 0.078056386 | -0.9816799 | -1.15238643 | -1.3348708 | -1.434427549 | -1.49591857 | -1.53615015 | -1.60086711 |
| AT4G27090 | 5.3219905 | 4.4249431 | 0.006255397 | -1.1296623 | -1.32381567 | -1.5512118 | -1.701991513 | -1.75823099 | -1.81293531 | -1.87016210 |
| AT1G56045 | 4.1265461 | 3.8013931 | 0.081949902 | -0.7611507 | -1.00883428 | -1.1740414 | -1.305814679 | -1.32739749 | -1.36705708 | -1.40193826 |
| AT5G27850 | 4.9486069 | 4.3240707 | -0.191237039 | -1.1429370 | -1.29665658 | -1.4495947 | -1.568391609 | -1.58415006 | -1.62066850 | -1.66361449 |
| AT3G02560 | 4.1414938 | 3.6324283 | 0.114630934 | -0.8004553 | -0.99355820 | -1.1443436 | -1.261804350 | -1.27392442 | -1.32918619 | -1.35199266 |
| AT3G25520 | 4.6023274 | 4.0387473 | -0.017835266 | -0.9581989 | -1.13737805 | -1.3189952 | -1.458921665 | -1.51155934 | -1.53587220 | -1.57481806 |
| AT1G22780 | 5.4168899 | 4.3761691 | 0.005704120 | -1.0896915 | -1.22533436 | -1.3521492 | -1.452643774 | -1.45722806 | -1.48745400 | -1.54190511 |
| AT5G58420 | 6.1514813 | 5.0818177 | 0.060803337 | -0.9963555 | -1.21786683 | -1.3621342 | -1.486700552 | -1.53436320 | -1.56955572 | -1.59090436 |
| AT1G17285 | 1.6325749 | 2.4238939 | 2.946607675 | 1.4195383 | 0.99698094 | 0.2849380 | -0.222638715 | -0.55796075 | -0.75473131 | -0.78760903 |
| AT5G14020 | 0.9988840 | 1.5719543 | 2.589507503 | 1.7451860 | 1.50660433 | 0.7071862 | 0.001890851 | -0.61821259 | -0.82081396 | -0.88111036 |
| AT2G24280 | 0.8123856 | 1.2868378 | 1.748959390 | 0.9226257 | 0.71953032 | 0.3508008 | 0.130061805 | -0.02054685 | -0.08388366 | -0.07564624 |
| AT1G54000 | 0.6831540 | 0.6413816 | 1.824268765 | 1.2858661 | 0.70363342 | 0.0130056 | -1.025801594 | -1.50244121 | -1.74456840 | -1.63801288 |
| AT1G32190 | 2.4876543 | 2.6718260 | 2.117170382 | 1.3912299 | 0.98882962 | 0.3993983 | -0.180577525 | -0.35945728 | -0.34673378 | -0.34883379 |
| AT3G19820 | 1.7004443 | 2.7697936 | 4.161620765 | 2.8243545 | 1.90265264 | 1.1560632 | -0.064870255 | -0.68281676 | -0.92049556 | -0.98320564 |
| AT1G26945 | 0.1855114 | 0.7098123 | 1.946718754 | 1.6403748 | 1.40327453 | 0.7383544 | -0.053394961 | -0.43028766 | -0.48110573 | -0.49928227 |
| AT1G62810 | 0.5479245 | 1.0322627 | 1.607207351 | 0.6944904 | 0.42579520 | 0.2197674 | -0.061714949 | -0.10569089 | -0.04563733 | 0.04739972 |
| AT2G45050 | 1.6793998 | 2.6796167 | 3.433404661 | 0.9839113 | 0.10362365 | -0.8877786 | -1.285458636 | -1.33661885 | -1.35485756 | -1.35696932 |
| AT2G20515 | 2.8798592 | 3.4300523 | 2.393420845 | 0.5070670 | -0.01738539 | -0.4343897 | -0.621503108 | -0.64727459 | -0.64181123 | -0.64228395 |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| AT4G30190 | -0.8222151 | -0.71308906 | 0.547734155 | 1.9185150861 | 2.153623989 | 2.774670662 | 2.721294556 | 2.1574153 | 1.5172489 | 1.6990466 |
| AT2G39010 | -0.8139579 | -0.67626689 | 2.026462580 | 4.0015520971 | 5.126804381 | 6.287168344 | 6.894412728 | 4.8370105 | 2.7223877 | 1.8985461 |
| AT5G64620 | -0.4716171 | -0.43842360 | 1.371077821 | 3.6439026942 | 4.676059864 | 5.523951227 | 5.628490676 | 3.9425602 | 2.2505642 | 2.2379515 |
| AT5G66920 | -0.7473664 | -0.65055467 | 0.553446198 | 2.1486002344 | 2.462291078 | 3.186697917 | 3.302314359 | 2.4521441 | 1.1240185 | 0.9309736 |
| AT3G21670 | -0.2335829 | 0.04102029 | 1.529240304 | 2.2943438276 | 2.562045900 | 2.404527983 | 2.326697404 | 1.6644404 | 0.9748708 | 1.2192169 |
| AT4G25830 | -0.8471250 | -0.91139702 | -0.567159093 | -0.2072573097 | 0.064841310 | 0.555590275 | 1.600543257 | 3.1054826 | 3.7737804 | 4.0987657 |
| AT3G57020 | -1.3261087 | -1.28628942 | 0.019712843 | 1.5809823490 | 1.951262142 | 2.852295726 | 3.904178517 | 5.8760458 | 7.1078994 | 8.0188040 |
| AT4G23400 | -1.6189207 | -1.63947830 | -1.025042277 | -0.0532276043 | 0.501373587 | 1.352312457 | 3.374835389 | 5.6359847 | 6.9700095 | 7.6733581 |
| AT4G02700 | -0.2927995 | -0.32901222 | -0.104593336 | 0.0796793157 | -0.008197751 | 0.168664647 | 0.570563028 | 1.6260180 | 2.1607804 | 2.6013351 |
| AT4G00330 | -0.5142283 | -0.58494483 | -0.528194500 | -0.3654327146 | -0.360308224 | -0.212730648 | 0.379753767 | 1.3213993 | 1.4932740 | 1.0615307 |
| AT3G14690 | -0.4059807 | -0.26135001 | 0.072725588 | 0.4143861589 | 0.564499296 | 0.833333701 | 1.953636202 | 3.9122874 | 4.6568164 | 6.0095359 |
| AT5G25810 | -0.3404144 | -0.31705585 | -0.292849274 | -0.2405119713 | -0.225564837 | -0.161728863 | 0.272805242 | 1.9855277 | 2.4754762 | 2.5196483 |
| AT1G66725 | -0.8413585 | -0.88074266 | -0.672666618 | -0.5263664934 | -0.425877187 | -0.173234296 | 0.950211683 | 1.8942547 | 2.0066724 | 1.6682482 |
| AT2G31570 | -1.2301238 | -1.18916807 | -0.818707686 | -0.6774019433 | -0.647406013 | -0.557148160 | -0.157165103 | 1.0827289 | 3.0171150 | 3.1806977 |
| AT4G37010 | -1.1426906 | -1.04851771 | -0.176408945 | 0.0106280991 | 0.223705129 | 0.357114240 | 1.338770039 | 3.3656682 | 5.5192869 | 5.4216938 |
| AT5G15180 | -1.0923623 | -1.09343550 | -0.883423969 | -0.7943016232 | -0.731386438 | -0.573229362 | 0.683180875 | 4.4848112 | 7.8387598 | 9.1738217 |
| AT5G44130 | -0.5068211 | -0.50476819 | -0.460284177 | -0.2870945664 | -0.196276140 | -0.007526504 | 0.685202305 | 2.5798811 | 4.5167909 | 5.2872617 |
| AT5G53370 | -0.5807505 | -0.56375986 | -0.074017693 | 0.4433051226 | 0.597628910 | 1.077355395 | 2.489457155 | 4.6555237 | 6.0946946 | 7.4280850 |
| AT5G63600 | -1.4076945 | -1.34426199 | -0.950976607 | -0.8536102760 | -0.825039383 | -0.496535257 | 0.894586565 | 2.3451309 | 3.0851778 | 3.2928712 |
| AT3G28940 | -0.8267220 | -0.86126587 | -0.620511067 | -0.5052665695 | -0.411478638 | -0.322854972 | -0.052691485 | 0.8990039 | 2.2812660 | 2.5188865 |
| AT4G09760 | 0.2979092 | 0.04599711 | -0.219205538 | -0.2687656356 | -0.279981082 | -0.205216469 | 0.273757302 | 2.0072180 | 3.4340299 | 3.8674314 |
| AT3G48890 | -0.4059805 | -0.42858406 | -0.267885962 | -0.0004057439 | -0.005243846 | 0.152895326 | 0.436089615 | 1.2495969 | 1.9688484 | 3.1484785 |
| AT5G19230 | -1.2179382 | -1.28815167 | -0.916802820 | -0.8915080597 | -0.855871406 | -0.619930529 | 0.169518899 | 1.9100807 | 3.2136827 | 4.9477881 |
| AT3G18170 | -0.4271698 | -0.50125792 | -0.262497291 | -0.2676837946 | -0.265512860 | -0.204452211 | 0.093003012 | 1.4245544 | 3.0627997 | 4.8484462 |
| AT4G25900 | -0.9813610 | -0.95350247 | -0.518273918 | -0.1892881499 | -0.169471213 | -0.029966340 | 0.005774842 | 0.3150573 | 0.6743071 | 1.1637587 |
| AT5G44380 | -2.0117815 | -1.97765704 | -1.490264836 | -1.1244348132 | -0.942767099 | -0.529873082 | 0.779433172 | 2.8213110 | 4.0644523 | 5.5585071 |
| AT2G27920 | -0.3505470 | -0.36880057 | -0.335433957 | -0.2534726802 | -0.282127762 | -0.221513501 | 0.027456556 | 1.1422515 | 2.9809897 | 4.4176378 |
| AT4G15610 | -1.4550514 | -1.50867435 | -1.046588167 | -0.8654570386 | -0.753390915 | -0.527470320 | 0.191034251 | 1.6526311 | 2.6269300 | 4.0501623 |
| AT3G17420 | -0.7956779 | -0.86764825 | -0.752382855 | -0.5957468266 | -0.587627111 | -0.444276601 | 0.148891346 | 1.4217575 | 2.0685579 | 3.2194249 |
| AT1G08930 | -0.6456934 | -0.71843189 | 0.007498428 | 0.3669447964 | 0.529562703 | 0.836792977 | 1.531232351 | 2.9947148 | 4.3550962 | 5.7712578 |
# annotation bar for consensus time
col_fun <- brewer.pal(10,"Spectral")
names(col_fun) <- c("T0", "T1", "T2", "T3", "T4", "T5", "T6", "T7", "T8", "T9")
col_fun
ha = HeatmapAnnotation(`Consensus Time Group` = c("T0", "T1", "T2", "T3", "T4", "T5", "T6", "T7", "T8", "T9"), col = list(`Consensus Time Group` = col_fun), show_legend = F)
# quantile normalize
mat = cor_sub_m
mat2 = t(apply(mat, 1, function(x) {
q10 = quantile(x, 0.1)
q90 = quantile(x, 0.9)
x[x < q10] = q10
x[x > q90] = q90
scale(x)
}))
colnames(mat2) = colnames(mat)
# side annotation to match cortex colors
cortex_sa = rowAnnotation(foo = anno_block(gp = gpar(fill = "#82B6FF"),
labels = c("Cortex"),
labels_gp = gpar(col = "black", fontsize = 18)))
feature_names %>% filter(gene == "AT1G09750")
| gene | Name |
|---|---|
| <chr> | <chr> |
| AT1G09750 | CORTEX |
# genes to label on side of heatmap for cortex
(cor_mat_for_mark <- data.frame(mat2) %>%
rownames_to_column("gene") %>%
left_join(feature_names) %>%
mutate(index=dplyr::row_number()) %>%
select(Name, index) %>%
filter(Name %in% c("AT1G17285", "CYP75B1", "NPF6.4", "PER69", "AT4G09760")))
Joining, by = "gene"
| Name | index |
|---|---|
| <chr> | <int> |
| AT1G17285 | 21 |
| CYP75B1 | 45 |
| NPF6.4 | 65 |
| AT4G09760 | 81 |
# at - index of genes you want to mark
# labels - Names to show
cor_mark_anno = rowAnnotation(foo = anno_mark(at = cor_mat_for_mark$index, labels = cor_mat_for_mark$Name, labels_gp = gpar(col = "black", fontsize = 16)))
# ['#d8b365','#f5f5f5','#5ab4ac']
options(repr.plot.width=10, repr.plot.height=8)
Cortex_hm <- Heatmap(mat2,
col = colorRamp2(c(-1.5, 0, 1.5),
c('blue','white','red')),
show_column_names = F,
cluster_columns = F,
cluster_rows=F,
show_row_names = F,
show_heatmap_legend = F,
left_annotation=cortex_sa,
right_annotation=cor_mark_anno)
draw(Cortex_hm, padding = unit(c(10, 10, 10, 10), "mm"), heatmap_legend_side = "top")
# text annotation for consensus time
ht = columnAnnotation(foo = anno_text(c("T0", "T1", "T2", "T3", "T4", "T5", "T6", "T7", "T8", "T9"), rot = 0, just = "center", gp = gpar(fontsize = 16)))
options(repr.plot.width=12, repr.plot.height=10)
ht_list = ht %v% ha %v% Endo_hm %v% Cortex_hm
draw(ht_list, ht_gap = unit(0.2, "cm"), padding = unit(c(2, 2, 5, 10), "mm"), heatmap_legend_side = "bottom")
# grab heatmap as a grob to arrange in cowplot
hm_final <- grid.grabExpr(draw(ht_list, ht_gap = unit(0.2, "cm"), padding = unit(c(2, 2, 5, 10), "mm"), heatmap_legend_side = "bottom"))## bottom, left, top and right
# output heatmap as pdf
pdf("./supp_data/WT_Ground_tissue_heatmap.pdf", width = 12, height = 10)
draw(ht_list, ht_gap = unit(0.2, "cm"), padding = unit(c(2, 2, 5, 10), "mm"), heatmap_legend_side = "bottom") ## bottom, left, top and right
dev.off()
options(repr.plot.width=8, repr.plot.height=6)
DefaultAssay(rc.integrated) <- "integrated"
(SCR <- FeaturePlot(rc.integrated, features = "AT3G54220",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("SCR"))
(MYB36 <- FeaturePlot(rc.integrated, features = "AT5G57620",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = F, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("MYB36"))
(CASP <- FeaturePlot(rc.integrated, features = "AT2G36100",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("CASP1"))
options(repr.plot.width=8, repr.plot.height=6)
(Cor_1 <- FeaturePlot(rc.integrated, features = "AT1G17285",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("AT1G17285"))
options(repr.plot.width=8, repr.plot.height=6)
(Cor_2 <- FeaturePlot(rc.integrated, features = "AT5G64620",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("C/VIF2"))
options(repr.plot.width=8, repr.plot.height=6)
(Cor_3 <- FeaturePlot(rc.integrated, features = "AT4G09760",
cols = c("grey", "red"), label=F, repel=F, pt.size = 0.3, order = T, min.cutoff = "q1", max.cutoff = "q99") + ggtitle("AT4G09760"))
plot_anno <- function(rc.integrated){
order <- c("Quiescent Center", "Ground Tissue","Columella", "Lateral Root Cap", "Atrichoblast", "Trichoblast", "Cortex", "Endodermis", "Metaphloem & Companion Cell","Protophloem", "Xylem", "Procambium","Xylem Pole Pericycle","Phloem Pole Pericycle", "Protoxylem", "Metaxylem", "Unknown")
palette <- c("#9400d3", "#DCD0FF","#5ab953", "#bfef45", "#008080", "#21B6A8", "#82b6ff", "#0000FF","#e6194b", "#dd77ec", "#9a6324", "#ffe119", "#ff9900", "#ffd4e3", "#9a6324", "#ddaa6f", "#EEEEEE")
rc.integrated$celltype.anno <- factor(rc.integrated$celltype.anno, levels = order[sort(match(unique(rc.integrated$celltype.anno),order))])
color <- palette[sort(match(unique(rc.integrated$celltype.anno),order))]
p1 <- DimPlot(rc.integrated, reduction = "umap", group.by = "celltype.anno", cols=color) + ggtitle("Cell Type") + theme(plot.title = element_text(hjust = 0.5))
p2 <- DimPlot(rc.integrated, reduction = "umap", group.by = "time.anno",order = c("Distal Columella","Proximal Columella","Distal Lateral Root Cap","Proximal Lateral Root Cap","Maturation","Elongation","Meristem"),cols = c("#e5f5e0", "#a1d99b", "#31a354", "#deebf7", "#3182bd", '#fee0d2','#de2d26')) + ggtitle("Developmental Stage") + theme(plot.title = element_text(hjust = 0.5))
p3 <- DimPlot(rc.integrated, reduction = "umap", group.by = "consensus.time.group", cols=brewer.pal(10,"Spectral")) + ggtitle("Consensus Time") + theme(plot.title = element_text(hjust = 0.5))
options(repr.plot.width=25, repr.plot.height=8)
gl <- lapply(list(p1, p2, p3), ggplotGrob)
gwidth <- do.call(unit.pmax, lapply(gl, "[[", "widths"))
gl <- lapply(gl, "[[<-", "widths", value = gwidth)
gridExtra::grid.arrange(grobs=gl, ncol=3)
}
options(repr.plot.width=28, repr.plot.height=6)
top_umaps <- plot_anno(rc.integrated)
options(repr.plot.width=24, repr.plot.height=18)
gene_umaps <- plot_grid(SCR, MYB36, CASP, Cor_1, Cor_2, Cor_3, ncol=3, align="hv")
gene_hm <- plot_grid(gene_umaps, hm_final, ncol=2, rel_widths = c(1.6, 1))
options(repr.plot.width=28, repr.plot.height=18)
plot_grid(top_umaps, gene_hm, ncol=1, rel_heights = c(1, 1.5))
ggsave("./supp_data/Endo_cortex_traj_combined.pdf",
width = 28,
height = 18)
sessionInfo()
R version 4.0.3 (2020-10-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /fast/home/c/chsu/anaconda3/envs/seu3/lib/libopenblasp-r0.3.12.so locale: [1] LC_CTYPE=en_US.utf-8 LC_NUMERIC=C [3] LC_TIME=en_US.utf-8 LC_COLLATE=en_US.utf-8 [5] LC_MONETARY=en_US.utf-8 LC_MESSAGES=en_US.utf-8 [7] LC_PAPER=en_US.utf-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ggrepel_0.8.2 circlize_0.4.12 ComplexHeatmap_2.6.2 [4] cowplot_1.1.0 future_1.20.1 RColorBrewer_1.1-2 [7] Seurat_3.1.5 forcats_0.5.0 stringr_1.4.0 [10] dplyr_1.0.2 purrr_0.3.4 readr_1.4.0 [13] tidyr_1.1.2 tibble_3.0.4 ggplot2_3.3.2 [16] tidyverse_1.3.0 loaded via a namespace (and not attached): [1] Rtsne_0.15 colorspace_2.0-0 rjson_0.2.20 [4] ellipsis_0.3.1 ggridges_0.5.2 IRdisplay_0.7.0 [7] GlobalOptions_0.1.2 base64enc_0.1-3 fs_1.5.0 [10] clue_0.3-58 rstudioapi_0.13 farver_2.0.3 [13] leiden_0.3.5 listenv_0.8.0 fansi_0.4.1 [16] lubridate_1.7.9 xml2_1.3.2 codetools_0.2-18 [19] splines_4.0.3 IRkernel_1.1.1.9000 jsonlite_1.7.1 [22] Cairo_1.5-12.2 broom_0.7.2 ica_1.0-2 [25] cluster_2.1.0 dbplyr_2.0.0 png_0.1-7 [28] uwot_0.1.8 sctransform_0.3.1 compiler_4.0.3 [31] httr_1.4.2 backports_1.2.0 assertthat_0.2.1 [34] Matrix_1.2-18 lazyeval_0.2.2 cli_2.1.0 [37] htmltools_0.5.0 tools_4.0.3 rsvd_1.0.3 [40] igraph_1.2.6 gtable_0.3.0 glue_1.4.2 [43] RANN_2.6.1 reshape2_1.4.4 Rcpp_1.0.5 [46] cellranger_1.1.0 vctrs_0.3.4 ape_5.4-1 [49] nlme_3.1-150 lmtest_0.9-38 globals_0.13.1 [52] ps_1.4.0 rvest_0.3.6 lifecycle_0.2.0 [55] irlba_2.3.3 MASS_7.3-53 zoo_1.8-8 [58] scales_1.1.1 hms_0.5.3 parallel_4.0.3 [61] reticulate_1.18 pbapply_1.4-3 gridExtra_2.3 [64] stringi_1.5.3 S4Vectors_0.28.0 BiocGenerics_0.36.0 [67] shape_1.4.5 repr_1.1.0 rlang_0.4.8 [70] pkgconfig_2.0.3 matrixStats_0.57.0 evaluate_0.14 [73] lattice_0.20-41 ROCR_1.0-11 labeling_0.4.2 [76] patchwork_1.1.0 htmlwidgets_1.5.2 tidyselect_1.1.0 [79] parallelly_1.21.0 RcppAnnoy_0.0.16 plyr_1.8.6 [82] magrittr_1.5 R6_2.5.0 IRanges_2.24.0 [85] generics_0.1.0 pbdZMQ_0.3-3.1 DBI_1.1.0 [88] pillar_1.4.6 haven_2.3.1 withr_2.3.0 [91] fitdistrplus_1.1-1 survival_3.2-7 future.apply_1.6.0 [94] tsne_0.1-3 modelr_0.1.8 crayon_1.3.4 [97] uuid_0.1-4 KernSmooth_2.23-18 plotly_4.9.2.1 [100] GetoptLong_1.0.5 readxl_1.3.1 data.table_1.13.2 [103] reprex_0.3.0 digest_0.6.27 stats4_4.0.3 [106] munsell_0.5.0 viridisLite_0.3.0